X Chromosome

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Human X chromosome

Humans have 23 pairs of chromosomes, 22 autosomes and a pair of sex chromosomes. Females have a pair of X chromosomes (46, XX) and males have one X and one Y Chromosome (46, XY). This section of notes introduces the X chromosome and its role in development.

There is a separate page discussing X Inactivation that occurs in all female development with one of the X chromosomes to provide the correct gene dosage. There is a separate page discussing Trisomy X, a genetic disorder where there is an additional copy of the X chromosome. There is a separate page discussing Fragile X Syndrome, a genetic disorder where part of the X chromosome is lost.

  • Genes such as WNT4 (Wingless-Type Mmtv Integration Site Family, Member 4), NR0B1 (Nuclear Receptor Subfamily 0, Group B, Member 1; Dax-1) necessary for initiation of female pathway ovary development
  • An early discovery (1961) was that in order to have correct levels of X chromosome gene/protein expression (gene dosage), females must "inactivate" a single copy of the X chromosome in each and every cell. The initiator of the X inactivation process was discovered (1991) to be regulated by a region on the inactivating X chromosome encoding an X inactive specific transcript (XIST), that acts as RNA and does not encode a protein.
  • The genetic content of the X chromosome has been strongly conserved between species because these genes have become adapted to working as a single dose - Ohno's law
  • X inactivation occurs randomly throughout the embryo, generating a mosaic of maternal and paternally derived X chromosome activity in all tissues and organs. This can be seen in the fur colour of tortoiseshell cats.

Nucleus structure cartoon 01.jpg Chromatin Structure.png
Chromosome territories (interphase) Chromosome (Chromatin) structure (mitosis)

X Chromosome Links: X chromosome | X Inactivation | Trisomy X | Fragile X syndrome | Klinefelter syndrome | primordial germ cell | Female | epigenetics | Y chromosome | 2011 Group Project - Fragile X Syndrome | Category:X Chromosome
Genital Links: genital | Lecture - Medicine | Lecture - Science | Lecture Movie | Medicine - Practical | primordial germ cell | meiosis | endocrine gonad‎ | Genital Movies | genital abnormalities | Assisted Reproductive Technology | puberty | Category:Genital
Female | X | X inactivation | ovary | corpus luteum | oocyte | uterus | vagina | reproductive cycles | menstrual cycle | Category:Female
Male | Y | SRY | testis | spermatozoa | ductus deferens | penis | prostate | Category:Male
Historic Embryology - Genital 
General: 1901 Urinogenital Tract | 1902 The Uro-Genital System | 1904 Ovary and Testis | 1912 Urinogenital Organ Development | 1914 External Genitalia | 1921 Urogenital Development | 1921 External Genital | 1942 Sex Cords | 1953 Germ Cells | Historic Embryology Papers | Historic Disclaimer
Female: 1904 Ovary and Testis | 1904 Hymen | 1912 Urinogenital Organ Development | 1914 External Genitalia | 1914 Female | 1921 External Genital | 1927 Female Foetus 15 cm | 1927 Vagina | 1932 Postnatal Ovary
Male: 1887-88 Testis | 1904 Ovary and Testis | 1904 Leydig Cells | 1906 Testis vascular | 1909 Prostate | 1912 Prostate | 1914 External Genitalia | 1915 Cowper’s and Bartholin’s Glands | 1920 Wolffian tubules | 1935 Prepuce | 1935 Wolffian Duct | 1942 Sex Cords | 1943 Testes Descent | Historic Embryology Papers | Historic Disclaimer
Human Chromosomes: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | X | Y  

Human idiogram.jpg

Human idiogram

Some Recent Findings

X and Y chromosomes
  • Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line[1] "Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state. Here we explain how evolution has influenced the gene content and germ line specialization of the mammalian sex chromosomes. We discuss new research uncovering unusual X dosage compensation states in germ cells, which we postulate influence sexual dimorphisms in germ line development and cause infertility in individuals with sex chromosome aneuploidy."
More recent papers  
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<pubmed limit=5>X Chromosome</pubmed>

X Chromosome Overview

  • 1400+ genes
  • 150 million base pairs
  • Contains about 5% of the haploid genome.
  • Genes encode house-keeping and specialized functions.
  • Conserved in gene content between species.
  • In females, one of the X-chromosomes is inactivated in each and every cell (known since 1961).
    • This inactivation occurs during embryogenesis.
    • X Inactivation appears to be random in somatic cells. (mosaic pattern)
    • The process starts at the "X inactivation centre" and spreads along the chromosome.

Chromosome Statistics

May 2012 (EST)

Length (bps) 155,270,560
Known Protein-coding Genes 812
Novel Protein-coding Genes 24
Pseudogene Genes 780
miRNA Genes 128
rRNA Genes 22
snRNA Genes 85
snoRNA Genes 64
Misc RNA Genes 52
SNPs 2,172,609

Ohno's law

Ohno's law is a genetic evolutionary theory that suggests that the mammalian X chromosomes are conserved among species. Named after Susumu Ohno (大野 乾 (1928 – 2000) a Japanese-American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.

Links: Biography | PMID 13730522 | PubMed OHNO S


Contrary to the above theory, the human X chromosome long arm genes are found on the monotreme X chromosome while the short arm genes are found distributed on the autosomes.

Links: Echidna | Platypus | Kangaroo | Koala |

Genetic Inheritance

The follow cartoons show how genes located on the X chromosome can have different potential inheritance patterns.

X-Linked dominant (affected father)

X-Linked dominant (affected father)

X-Linked dominant (affected mother)

X-Linked dominant (affected mother)

X-Linked recessive (affected father)

X-Linked recessive (affected father)

X-Linked recessive (carrier mother)

X-Linked recessive (carrier mother)

Inheritance Pattern images: Genetic Abnormalities | autosomal dominant | autosomal recessive | X-linked dominant (affected father) | X-Linked dominant (affected mother) | X-Linked recessive (affected father) | X-Linked recessive (carrier mother) | mitochondrial inheritance | Codominant inheritance | Genogram symbols | Genetics

Developmental Genes


Table - Human Bmp Family
Approved Name Previous
Synonyms Chromosome
BMP15 bone morphogenetic protein 15 GDF9B Xp11.22
    Links: Developmental Signals - Bone Morphogenetic Protein | OMIM BMP2 | HGNC | Bmp Family | Sox Family | Tbx Family
Human BMP Family  
Table - Human Bmp Family
Approved Name Previous
Synonyms Chromosome
BMP1 bone morphogenetic protein 1 PCOLC 8p21.3
BMP2 bone morphogenetic protein 2 BMP2A 20p12.3
BMP3 bone morphogenetic protein 3 4q21.21
BMP4 bone morphogenetic protein 4 BMP2B 14q22.2
BMP5 bone morphogenetic protein 5 6p12.1
BMP6 bone morphogenetic protein 6 VGR VGR1 6p24.3
BMP7 bone morphogenetic protein 7 OP-1 20q13.31
BMP8A bone morphogenetic protein 8a 1p34.3
BMP8B bone morphogenetic protein 8b BMP8 OP-2 1p34.2
BMP10 bone morphogenetic protein 10 2p13.3
BMP15 bone morphogenetic protein 15 GDF9B Xp11.22
    Links: Developmental Signals - Bone Morphogenetic Protein | OMIM BMP2 | HGNC | Bmp Family | Sox Family | Tbx Family


Table - Human Sox Family
Approved Name Previous Symbols Synonyms Chromosome
SOX3 SRY-box 3 PHP Xq27.1
    Links: Developmental Signals - Sox | OMIM | HGNC | Tbx Family
Human SOX Family  
Table - Human Sox Family
Approved Name Previous Symbols Synonyms Chromosome
SOX1 SRY-box 1 13q34
SOX2 SRY-box 2 3q26.33
SOX3 SRY-box 3 PHP Xq27.1
SOX4 SRY-box 4 6p22.3
SOX5 SRY-box 5 "L-SOX5, MGC35153" 12p12.1
SOX6 SRY-box 6 11p15.3
SOX7 SRY-box 7 8p23.1
SOX8 SRY-box 8 16p13.3
SOX9 SRY-box 9 "CMD1, CMPD1" SRA1 17q24.3
SOX10 SRY-box 10 "DOM, WS4, WS2E" 22q13.1
SOX11 SRY-box 11 2p25.2
SOX12 SRY-box 12 SOX22 20p13
SOX13 SRY-box 13 "Sox-13, ICA12, MGC117216" 1q32.1
SOX14 SRY-box 14 SOX28 3q22.3
SOX15 SRY-box 15 SOX20 "SOX27, SOX26" 17p13.1
SOX17 SRY-box 17 8q11.23
SOX18 SRY-box 18 20q13.33
SOX21 SRY-box 21 SOX25 13q32.1
SOX30 SRY-box 30 5q33.3
SRY sex determining region Y TDF Yp11.2
    Links: Developmental Signals - Sox | OMIM | HGNC | Tbx Family | Bmp Family | Fgf Family | Pax Family | R-spondin Family | Sox Family | Tbx Family


Table - Human Tbx Family
Approved Name Previous Symbols Synonyms Chromosome
TBX22 T-box 22 "CPX, CLPA" Xq21.1
    Links: Developmental Signals - Tbx | OMIM Tbx3 | HGNC | Bmp Family | Sox Family | Tbx Family
Human TBX Family  
Table - Human Tbx Family
Approved Name Previous Symbols Synonyms Chromosome
TBX1 T-box 1 VCF CATCH22 22q11.21
TBX2 T-box 2 17q23.2
TBX3 T-box 3 UMS "TBX3-ISO, XHL" 12q24.21
TBX4 T-box 4 17q23.2
TBX5 T-box 5 HOS 12q24.21
TBX6 T-box 6 16p11.2
TBX10 T-box 10 TBX7 TBX13 11q13.2
TBX15 T-box 15 TBX14 1p12
TBX18 T-box 18 6q14.3
TBX19 T-box 19 "dj747L4.1, TPIT" 1q24.2
TBX20 T-box 20 7p14.2
TBX21 T-box 21 "TBLYM, T-bet" 17q21.32
TBX22 T-box 22 "CPX, CLPA" Xq21.1
TBX23P T-box 23, pseudogene TBX23 1q25
TBR1 T-box, brain 1 2q24.2
EOMES eomesodermin TBR2 3p24.1
MGA MGA, MAX dimerization protein "KIAA0518, MAD5, MXD5, FLJ12634" 15q15
TBXT T-box transcription factor T T 6q27
    Links: Developmental Signals - Tbx | OMIM Tbx3 | HGNC | Bmp Family | Sox Family | Tbx Family



Selected Female Infertility Genes
Gene abbreviation Name Gene Location Online Mendelian
Inheritance in Man (OMIM)
HUGO Gene Nomenclature
Committee (HGNC)
GeneCards (GCID) Diagnosis
BMP15 Bone morphogenetic protein 15 Xp11.22 300247 1068 GC0XP050910 Primary ovarian insufficiency
CLPP Caseinolytic mitochondrial matrix peptidase proteolytic subunit 19p13.3 601119 2084 GC19P006369 Primary ovarian insufficiency
EIF2B2 Eukaryotic translation initiation factor 2B subunit beta 14q24.3 606454 3258 GC14P075002 Primary ovarian insufficiency
FIGLA Folliculogenesis-specific BHLH transcription factor 2p13.3 608697 24669 GC02M070741 Primary ovarian insufficiency
FMR1 Fragile X mental retardation 1 Xq27.3 309550 3775 GC0XP147912 Primary ovarian insufficiency
FOXL2 Forkhead box L2 3q22.3 605597 1092 GC03M138944 Primary ovarian insufficiency
FSHR Follicle stimulating hormone receptor 2p16.3 136435 3969 GC02M048866 Primary ovarian insufficiency
GALT Galactose-1-phosphate uridylyltransferase 9p13.3 606999 4135 GC09P034636 Primary ovarian insufficiency
GFD9 Growth differentiation factor 9 5q31.1 601918 4224 GC05M132861 Primary ovarian insufficiency
HARS2 Histidyl-TRNA synthetase 2, mitochondrial 5q31.3 600783 4817 GC05P141975 Primary ovarian insufficiency
HFM1 HFM1, ATP-dependent DNA helicase homolog 1p22.2 615684 20193 GC01M091260 Primary ovarian insufficiency
HSD17B4 Hydroxysteroid 17-beta dehydrogenase 4 5q23.1 601860 5213 GC05P119452 Primary ovarian insufficiency
LARS2 Leucyl-TRNA synthetase 2, mitochondrial 3p21.31 604544 17095 GC03P045405 Primary ovarian insufficiency
LHCGR Luteinizing hormone/choriogonadotropin receptor 2p16.3 152790 6585 GC02M048647 Primary ovarian insufficiency
LHX8 LIM homeobox 8 1p31.1 604425 28838 GC01P075128 Primary ovarian insufficiency
MCM8 Minichromosome maintenance 8 homologous recombination repair factor 20p12.3 608187 16147 GC20P005926 Primary ovarian insufficiency
  Table data source[2] (table 1)    Links: fertilization | oocyte | ovary | | Female Infertility Genes | spermatozoa | testis | Male Infertility Genes | Genetic Abnormalities | ART

 Primary ovarian insufficiency - depletion or dysfunction of ovarian follicles with cessation of menses before age 40 years.
 Oocyte maturation arrest - arrest of human oocytes may occur at different stages of meiosis.


  1. Sangrithi MN & Turner JMA. (2018). Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line. Bioessays , , . PMID: 29756331 DOI.
  2. Harper JC, Aittomäki K, Borry P, Cornel MC, de Wert G, Dondorp W, Geraedts J, Gianaroli L, Ketterson K, Liebaers I, Lundin K, Mertes H, Morris M, Pennings G, Sermon K, Spits C, Soini S, van Montfoort APA, Veiga A, Vermeesch JR, Viville S & Macek M. (2018). Recent developments in genetics and medically assisted reproduction: from research to clinical applications. Eur. J. Hum. Genet. , 26, 12-33. PMID: 29199274 DOI.


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Emerson JJ, Kaessmann H, Betrán E & Long M. (2004). Extensive gene traffic on the mammalian X chromosome. Science , 303, 537-40. PMID: 14739461 DOI.

External Links

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Glossary Links

Glossary: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | Numbers | Symbols | Term Link
Human Chromosomes: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | X | Y  
Idiogram Chromosome Banding - The term refers to the light and dark pattern, seen after staining with a dye, of individual chromosomes identified in metaphase. It is only in meiosis and mitosis during metaphase that chromosomes can be easily identified, during the normal cell life (interphase) the chromosomes are unravelled and distributed within the nucleus in chromosome territories. A band is that part of a chromosome which is clearly distinguishable from nearby regions by appearing darker or brighter with one or more banding techniques.
Human Idiogram: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | X | Y
Genetic abnormality locations: 1-4 | 5-8 | 9-12 | 13-16 | 17-20 | 21-XY | sSMC
Inheritance Pattern images: Genetic Abnormalities | autosomal dominant | autosomal recessive | X-linked dominant (affected father) | X-Linked dominant (affected mother) | X-Linked recessive (affected father) | X-Linked recessive (carrier mother) | mitochondrial inheritance | Codominant inheritance | Genogram symbols | Genetics
Links: Genetics | Abnormal Development - Genetic

Cite this page: Hill, M.A. (2021, February 24) Embryology X Chromosome. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/X_Chromosome

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© Dr Mark Hill 2021, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G