RetrogeneDB ID: retro_cjac_3659

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01192774.1:2820..3223(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSCJAG00000010130
• Aliases: None
• Description: thioredoxin-like 4A [Source:HGNC Symbol;Acc:30551]

Sequence

>retro_cjac_3659
ATGTCACACACACTCCTGCACCTCCACAGCAGCTGGCAGGTGGACCAGCCCATCCTCCCAGAGGAGGACCACATGGTTGT
CATTCGCTTCTGCAATGACTGGGACTCCACATGCATGAAAATGGACAAGGTCTTGTACAGCATCATTGAGAAGGTTAAAG
ATTTTGCAGTTATTTTTCTTGTGGATATTACCAAAGTACCTGACTTCAACAAAATGTATGAGTTATATGATCCATGCACT
ATCAGGAACAAGCACATCATGATTGTCTTGGGGACTGGCAACAAGATTAACTGGGCAATGGAGGATAAGCAGGAGATGGT
GGATATTAGAGGGATCATGGACCATAGGGCCTTCAATGGAGGCACCTGGTCATGCCCTCAAAAACTACTCCATGAAGTAC
AAA

Alignment

ORF - retro_cjac_3659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFN
          MS..L.HLH..WQVDQ.IL.EED..VVIRF..DWD.TCMKMD.VLYSI.EKVK.FAVI.LVDIT.VPDFN
Retrocopy MSHTLLHLHSSWQVDQPILPEEDHMVVIRFCNDWDSTCMKMDKVLYSIIEKVKDFAVIFLVDITKVPDFN

Parental  KMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKG-RGLVVSPK-DYST
          KMYELYDPCT.....RNKHIMI.LGTG..NKINWAMEDKQEMVDI.......A..G.R.LV...K..YS.
Retrocopy KMYELYDPCTI----RNKHIMIVLGTG--NKINWAMEDKQEMVDIRGIMDHRAFNG<RHLVMPSK<NYSM

Parental  KYR
          KY.
Retrocopy KYK

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	6.61 RPM
SRP051959_heart	0.00 RPM	6.51 RPM
SRP051959_kidney	0.07 RPM	7.17 RPM
SRP051959_liver	0.00 RPM	7.06 RPM
SRP051959_lung	0.65 RPM	5.25 RPM
SRP051959_lymph_node	0.02 RPM	7.12 RPM
SRP051959_skeletal_muscle	0.02 RPM	11.79 RPM
SRP051959_spleen	0.02 RPM	6.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3659 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659 ,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,