RetrogeneDB ID: retro_cjac_1655

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:2342487..2343213(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035254
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HOXA13
• Ensembl ID: ENSCJAG00000008192
• Aliases: None
• Description: None

Sequence

>retro_cjac_1655
CCTGGCCCGGCGGGCCCGGCAGGCACAGAGGCCGCGAAGCAATGCAGCCCCTGCTCCTTGGGGCCCGCGGCGCTGCGCTG
TGGCTATTTCGGCAGCGGCCACTACCCGTGCGCCCGCAGGGGCCCCGCACCCCAACGCTATCAAGTGGTGCGCGCAGCCC
GCCTCGGCCGCCGCCGCCGCCTTGGCCGACAAGTACGTGGATACCGCCGGCCCAGCGGCCGGGGAGTTCAGCTCCGCGCT
AAGGAGTTCGCCTTCTACCATCAGGGCTACGCAGCCGGGCCTTACCACCATCATCAGCCCATGCCTGGCTACCTGGATAT
GCCCGTGGTGCCGGGTCTCGGGGGCCCCGGCGACTCGCGCCACGAGCCCCTGGGTCTTCCCATGGAAAACTACCAGCCCT
GGGCGCTGCCCAACTGCTGGAACGGCCACATGTACTGCCCCAAAGAGCAGGCGCAGCCTCCCCACCTCTGGAAGTCCACT
CTGCCCGACGTGGTCTCCCATCCCTCGGATGCCAGCTCCTATAGGAGGGGGAGAAAGAAGCACGTGCCTTACACCAAGGT
GCAGTTAAAAGAACTTGAACGGGAATACGCCACGAACAAATTCATTACTAAGGACAAACGGAGGCGGGTATCAGCCACGA
CGAACCTCTCTGAGCGGCAGGTCACAATTTGGTTCCAGAGCAGGAGGGTTAAAGAGAAAAAAGTCATCAACAAACTGAAA
ACCACT

Alignment

ORF - retro_cjac_1655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.64 %
• Parental protein coverage: 94.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PATRGSAPGPAALPASPLIGSSSGPAALPXGYFGSGYDPCARMGP-HPNAIKSCAQPASAAAAAFADKYM
          P...G.A...AA...SP....S.GPAAL..GYFGSG..PCAR.GP.HPNAIK.CAQPASAAAAA.ADKY.
Retrocopy PGPAGPAGTEAAKQCSPC---SLGPAALRCGYFGSGHYPCARRGP>HPNAIKWCAQPASAAAAALADKYV

Parental  DTAGPAAEEFSS-RAKEFAFYHQGYAAGPYHHHQPMPGYLDMPVVPGLGGPGESRHEPLGLPMESYQPWA
          DTAGPAA.EFSS.RAKEFAFYHQGYAAGPYHHHQPMPGYLDMPVVPGLGGPG.SRHEPLGLPME.YQPWA
Retrocopy DTAGPAAGEFSS<RAKEFAFYHQGYAAGPYHHHQPMPGYLDMPVVPGLGGPGDSRHEPLGLPMENYQPWA

Parental  LPNGWNGQMYCPKEQAQPPHLWKSTLPDVVSHPSDASSYRRGRKKRVPYTKVQLKELEREYATNKFITKD
          LPN.WNG.MYCPKEQAQPPHLWKSTLPDVVSHPSDASSYRRGRKK.VPYTKVQLKELEREYATNKFITKD
Retrocopy LPNCWNGHMYCPKEQAQPPHLWKSTLPDVVSHPSDASSYRRGRKKHVPYTKVQLKELEREYATNKFITKD

Parental  KRRRISATTNLSERQVTIWFQNRRVKEKKVINKLKTT
          KRRR.SATTNLSERQVTIWFQ.RRVKEKKVINKLKTT
Retrocopy KRRRVSATTNLSERQVTIWFQSRRVKEKKVINKLKTT

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	4.33 RPM
SRP051959_heart	0.04 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.19 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.41 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1655 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1655 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008192	1 retrocopy	retro_cjac_1655 ,