RetrogeneDB ID: retro_cjac_1191

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:17222279..17223148(+)
• Located in intron of: ENSCJAG00000016433

Retrocopy information

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

Parental gene information

• Parental gene symbol: GATA6
• Ensembl ID: ENSCJAG00000020543
• Aliases: None
• Description: GATA binding protein 6 [Source:HGNC Symbol;Acc:4174]

Sequence

>retro_cjac_1191
GGCGGCAGCTGCAGCGTGGCAGCCATGGGCGGCTGCAAGCACCAGTACAGCTCGCTGTCGGCGGCGCGACCGCTGAACGG
GATGTACCACCACCACCACCCGAGCCCCTACTCGCCCTATGTGGGGGGCCGCTGACGCCCGCCTGGCCCGCCGGACCCTT
TGAAACCCCGGTGCTGCAGAGCCGTGCCGGAGCCCGCTCCCGGTGCCCCAGAGCCCTAGCACAGACCTGCTGGAGGACCT
GTCGAGAGCCGCGAGTGCATGAACTGCGGCTCCATCCAGATGCCGCTGTGGCGGCGGGACAGCACTGGCCACTACCTGTG
CAACGCCTGCGGGCTCTACAGCAAGATGAACAGCCTCAGTCGGCCCCTCATTAAGCCACAGAAGCGCGTGCCTTCATCAC
GGCAGCTTGGATTGTCCTGTGCCAACTGTTACACCACAACTACCACCTTATGGCGCAGAAATGCTGAGGGGGAATTCGCG
TGCAATGCTTGTGGACTCTATTGGAAACTCCATGGGGTGCCCAGACCACTTGCTATGAAAAAAGAAGGAATTCTAACCAG
GAAACGAAAACCTAAGAACATAAATAAATCAAAGACATGCTCTGGTAATAGCAATAATTACATTCCTATGACTCCAACTT
CCACCTCTTCTAACTCAGATGATTGCAGCAAAAATACTTCCCTACAACACAACCTACAGCCTCGGAGCGAGTGCCCCGGT
GATGACTGGCGCGGAAGAGCACTAATCCCGAGAACAGCGAGCTCAAGTATTCGGGGCAAGATGGGCTCTACATAGGCGTC
AGTCTGGCCTCACTGACCGAAGTCACATTCTCCGTGCAACAGGATTCCTGGTGCGCCCTGGTCCTGGCC

Alignment

ORF - retro_cjac_1191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.28 %
• Parental protein coverage: 66.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GGSGSLAAMGGREHQYSSLSAARPLNGTYHHHHHHHPSPYSPYVGA-PLTPAWPAGPFETPVLHSLQSRA
          GGS.S.AAMGG..HQYSSLSAARPLNG.Y...HHHHPSPYSPYVG..PLTPAWPAGPFETPV...LQSRA
Retrocopy GGSCSVAAMGGCKHQYSSLSAARPLNGMY---HHHHPSPYSPYVGG<PLTPAWPAGPFETPV---LQSRA

Parental  GA-PLPVPRGPSADLLEDLS-ESRECVNCGSIQTPLWRRDGTGHYLCNACGLYSKMNGLSRPLIKPQKRV
          GA.PLPVP..PS.DLLEDLS.ESREC.NCGSIQ.PLWRRD.TGHYLCNACGLYSKMN.LSRPLIKPQKRV
Retrocopy GA<PLPVPQSPSTDLLEDLS<ESRECMNCGSIQMPLWRRDSTGHYLCNACGLYSKMNSLSRPLIKPQKRV

Parental  PSSRRLGLSCANCHTTTTTLWRRNAEGEPVCNACGLYMKLHGVPRPLAM-KEGIQTRKRKPKNINKSKTC
          PSSR.LGLSCANC.TTTTTLWRRNAEGE..CNACGLY.KLHGVPRPLAM.KEGI.TRKRKPKNINKSKTC
Retrocopy PSSRQLGLSCANCYTTTTTLWRRNAEGEFACNACGLYWKLHGVPRPLAMKKEGILTRKRKPKNINKSKTC

Parental  SGNSNNSIPMTPTSTSSNSDDCSKNTS-PTTQPTAS-GASAPVMTGA-GESTNPENSELKYSG-QDGLYI
          SGNSNN.IPMTPTSTSSNSDDCSKNTS.PTTQPTAS.GASAPVMTGA.G....P........G.QDGLYI
Retrocopy SGNSNNYIPMTPTSTSSNSDDCSKNTS<PTTQPTAS<GASAPVMTGA<GRALIPRTASSSIRG<QDGLYI

Parental  GVSLASPAEVTSSVRQDSWCALALA
          GVSLAS..EVT.SV.QDSWCAL.LA
Retrocopy GVSLASLTEVTFSVQQDSWCALVLA

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	0.60 RPM	12.03 RPM
SRP051959_heart	0.81 RPM	52.74 RPM
SRP051959_kidney	0.29 RPM	1.49 RPM
SRP051959_liver	0.19 RPM	6.35 RPM
SRP051959_lung	0.52 RPM	14.06 RPM
SRP051959_lymph_node	0.53 RPM	2.17 RPM
SRP051959_skeletal_muscle	0.35 RPM	0.90 RPM
SRP051959_spleen	0.38 RPM	8.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1191 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1191 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	ENSCJAG00000020543	1 retrocopy	retro_cjac_1191 ,