RetrogeneDB ID: retro_cjac_1911

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:51998822..51999716(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004532
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SC5D
• Ensembl ID: ENSCJAG00000007436
• Aliases: None
• Description: sterol-C5-desaturase [Source:HGNC Symbol;Acc:10547]

Sequence

>retro_cjac_1911
ATGGACCTTGTACTCAGTGTTGCAGATTATTATTTTTTACACCATACATATATCCAGCTACATGGCCAGAAGATGACATC
CTCCGACAAGCTATTAGTCTTCTGATTACAGCAAATGTTGGTGCTTACATCCTTTATTTCTTCTGTGCAACATTGAGCTA
TTATTTTGTCTTTGATCATGCATTAATGAAACATCCACAATTTTTAAAGAATCAAGTCCGTCGAGAGATTAAGTTTACTG
TACAGGCATTGCCATGGATAAGTATACCTACTGTTTCACTGTTCCTGCTGGAGATAAGAGGTTACAGCAAGTTACATGAT
GACCTAGGAGAGTTTCCATATGGATTGCTTGAACTCGTTGTTAGTGTAATATCTTTCCTGTTTTTCACTGACATGTTCAT
CTACTGGATTCACAGAGGCCTTCATCATAGACTGGTATATAAGCACCTACATAAACCTCATCATGTTTGGAAGATTCCTA
CTCCATTTGCAAGTCACGCTTTTCACCCTGTCGATGGCTTTCTTCAGAGTCTACCTTACCATGTATACCCTTTTATCTTT
CCATTACACAAGGTGGTTTATTTAAGTCTGTACATCTTGGTTAATATCTGGACAATTTCCATTCATGATGATTTTCGTGT
CCCCCAAATCTTACAGCCATTTATTAATGGCTCAGCTCATCATACAGACCACCATATGTTCTTTGACTATAATTATGGAC
AGTATTTTTACTTTGTGGGATAGGATTGGAGGCTCATTCAAAAATCCTTCCTCCTTTGAGGGGAAGGGACCACTCAGTTA
TGTGAAGAACATGACAGAAAAAAAGTGCAGCAGCCATGCAGGAAATGGTTGTAAGAATGAAAAATTATTCAATGGAGCGT
TTACGAAGACTGAA

Alignment

ORF - retro_cjac_1911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDLVLSVADYYF-FTPYIYPATWPEDDILRQAISLLIIANVGAYILYFFCATLSYYFVFDHALMKHPQFL
          MDLVLSVADYYF.FTPYIYPATWPEDDILRQAISLLI.ANVGAYILYFFCATLSYYFVFDHALMKHPQFL
Retrocopy MDLVLSVADYYF<FTPYIYPATWPEDDILRQAISLLITANVGAYILYFFCATLSYYFVFDHALMKHPQFL

Parental  KNQVRREIKFTVQALPWISIPTVSLFLLEIRGYSKLHDDLGEFPYGLLELVVSVISFLFFTDMFIYWIHR
          KNQVRREIKFTVQALPWISIPTVSLFLLEIRGYSKLHDDLGEFPYGLLELVVSVISFLFFTDMFIYWIHR
Retrocopy KNQVRREIKFTVQALPWISIPTVSLFLLEIRGYSKLHDDLGEFPYGLLELVVSVISFLFFTDMFIYWIHR

Parental  GLHHRLVYKHLHKPHHVWKIPTPFASHAFHPVDGFLQSLPYHVYPFIFPLHKVVYLSLYILVNIWTISIH
          GLHHRLVYKHLHKPHHVWKIPTPFASHAFHPVDGFLQSLPYHVYPFIFPLHKVVYLSLYILVNIWTISIH
Retrocopy GLHHRLVYKHLHKPHHVWKIPTPFASHAFHPVDGFLQSLPYHVYPFIFPLHKVVYLSLYILVNIWTISIH

Parental  DGDFRVPQILQPFINGSAHHTDHHMFFDYNYGQY-FTLWDRIGGSFKNPSSFEGKGPLSYVKNMTEGKCS
          D.DFRVPQILQPFINGSAHHTDHHMFFDYNYGQY.FTLWDRIGGSFKNPSSFEGKGPLSYVKNMTE.KCS
Retrocopy D-DFRVPQILQPFINGSAHHTDHHMFFDYNYGQY>FTLWDRIGGSFKNPSSFEGKGPLSYVKNMTEKKCS

Parental  SHAGNGCTNEKLFNGEFTKTE
          SHAGNGC.NEKLFNG.FTKTE
Retrocopy SHAGNGCKNEKLFNGAFTKTE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	25.85 RPM
SRP051959_heart	0.05 RPM	26.78 RPM
SRP051959_kidney	0.13 RPM	32.30 RPM
SRP051959_liver	1.04 RPM	469.34 RPM
SRP051959_lung	0.10 RPM	16.28 RPM
SRP051959_lymph_node	0.07 RPM	10.46 RPM
SRP051959_skeletal_muscle	0.09 RPM	8.01 RPM
SRP051959_spleen	0.11 RPM	10.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1911 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1911 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019246	1 retrocopy	retro_btau_813,
Canis familiaris	ENSCAFG00000011805	1 retrocopy	retro_cfam_291,
Callithrix jacchus	ENSCJAG00000007436	1 retrocopy	retro_cjac_1911 ,
Monodelphis domestica	ENSMODG00000013028	1 retrocopy	retro_mdom_1086,
Mustela putorius furo	ENSMPUG00000005754	1 retrocopy	retro_mputfur_484,
Ochotona princeps	ENSOPRG00000003219	1 retrocopy	retro_opri_1143,
Ictidomys tridecemlineatus	ENSSTOG00000008946	1 retrocopy	retro_itri_964,
Tupaia belangeri	ENSTBEG00000000490	1 retrocopy	retro_tbel_4326,
Tarsius syrichta	ENSTSYG00000011139	1 retrocopy	retro_tsyr_1097,
Tursiops truncatus	ENSTTRG00000006908	1 retrocopy	retro_ttru_777,