RetrogeneDB ID: retro_cjac_1357

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:82595339..82596558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM214B
• Ensembl ID: ENSCJAG00000009210
• Aliases: None
• Description: family with sequence similarity 214, member B [Source:HGNC Symbol;Acc:25666]

Sequence

>retro_cjac_1357
AGTGCCACCTCTTCTTGGATTTCAGGGGCCTGGAGTCCCTCCTGGCCGCCATCATATGCTTCCTGCAATACTTTGCACAA
CAGAGACCAGGCTTTCCCAGAACCAGGGGACAAGGGTCCCTGGGGCAGTCCCCAGAGCCAGCCCTCTGGACCAGCTGCAC
ACACTTGACACTGATTTGCACAGTCTTGCACAAATGAGGGGTAAGAGCCCAGTGGCTAGGGTGGGCAATGGGGGAGCCTC
TGGCCTAGGGGAGTCCCCAAGCACTGCCAGTGGGCATGGTCTCAAGCACACACCCCCAGCCCTGGATCTCCAGGCCCCTG
CCCCACCAAGAGAAGGCTGCTTCCTGCTGGAGAAGCCCCAGATGTCAGCTCTGAGGAAGAGGAGCCACCCTTTGGAGGTG
CCAGGGAACCCTGGGCTACCCTACTGCTACTAACTGTTCTGATGCCCAAACCACACCCTCTGGAGACACCTTGCTGTCTG
GGCCCAAGAAGCACAGTTTCAGACCCAACAGACTGCATTCCCATGGGGCGGAGGCTGAGAGGTGCCTGTTGCCTAGAGCT
GGGCCCACTTCAAAGCCTCTGGAAGGGGCCAGGCCTGCTGAGTCTCCCCAGTGCCTCCCCTGTTCCTCCCCCTGCTGTCA
GTTGCACCCTGCGGGGCAACTTTGAGGATTTGTTGCTGCAAGGATGCTTTGCACCATCTGGCCACATTAAGGGCTTCACA
GCAGAGACTGGAGCTAGTGGGTCCTACTGCGTCCAGCATGTCACACTACCTGTCACCATCACCTTCTTTGAGGTTTCTGA
GCAAAATGCCCCCAACCCCACTGGGCCTTATGGAGCCGAACACCCTGGGGAGGAAGACTCACAGTGTGTCCAAAGTGGGC
ACCATCCAAATGACATTATTTAACCCCAACCAGACTGTGGTGAAGATGTTCCTGGTAATCTTTGACTTCTTGGGCATGGC
TGCTGCCCACATGCCCTTCCTGTGCAATCACCTCTTTTTGGTGCCTGTGGGTGAGGAGGAAAACGCTAACTCCACCCACT
GCCTTCTCTGCTATTCTCTGCACCTGAGGTTCCAGAACTCCCACTTAGGCCTCTTAAGCCTGAATAGAGATCTCCACCTG
CTTTTTTCCCACTAGAGCCTGGAGCTGGACACAGGGCTTCCCTACGAACTGCAGGCTGTAACTGAGGCCCCTCCTAATCC
ACGTTATTAGCCTTTGCCC

Alignment

ORF - retro_cjac_1357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 75.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SVTSSWTSGAWSPPCPPSNASCNTLHTRDWASPDPG-GQGSLGASPGPA-PPGQLHTIDTDLHSLAQIGG
          S.TSSW.SGAWSP..PPS.ASCNTLH.RD.A.P.PG.GQGSLG.SP.PA.P..QLHT.DTDLHSLAQ..G
Retrocopy SATSSWISGAWSPSWPPSYASCNTLHNRDQAFPEPG<GQGSLGQSPEPA<PLDQLHTLDTDLHSLAQMRG

Parental  KSPVAGVGNGR-SLWPR-ESPGTANGHSPEHTPPG-PGPPGPCPTKRRLLPAGEAPDINSEEE-GPAPRR
          KSPVA.VGNG..SLWPR.ESP.TA.GH...HTPP..PG.PGPCPTKRRLLPAGEAPD..SEEE.G....R
Retrocopy KSPVARVGNGG<SLWPR>ESPSTASGHGLKHTPPA<PGSPGPCPTKRRLLPAGEAPDVSSEEE<GATLWR

Parental  RRGTLGHPTAANSSDAKATPFWSHLLPGPKE-PVLDPTDCSPMGRRLKGARRLKLSPLRNLRKGPGLLSA
          ..GTLG.PTA.N.SDA..TP....LL.GPK...V.DPTDC.PMGRRL.GA..L.L.PL..L.KGPGLLS.
Retrocopy CQGTLGYPTATNCSDAQTTPSGDTLLSGPKK>TVSDPTDCIPMGRRLRGACCLELGPLQSLWKGPGLLSL

Parental  PSASPVPTPAVSRTLLGNFEESLLRERFAPSGHIEGFTAEIGASGSYCPQHVTLPVTVTFFDVSEQNA-P
          PSASPVP.PAVS.TL.GNFE..LL...FAPSGHI.GFTAE.GASGSYC.QHVTLPVT.TFF.VSEQNA.P
Retrocopy PSASPVPPPAVSCTLRGNFEDLLLQGCFAPSGHIKGFTAETGASGSYCVQHVTLPVTITFFEVSEQNA>P

Parental  APFLGVMDLKPLGRKGYSVPKVGTIQVTLFNPNQTVVKMFLVTFDFSDMPAAHMTFLRHRLFLVPVGEEG
          .P.LG.M....LGRK..SV.KVGTIQ.TLFNPNQTVVKMFLV.FDF..M.AAHM.FL...LFLVPVGEE.
Retrocopy TP-LGLMEPNTLGRKTHSVSKVGTIQMTLFNPNQTVVKMFLVIFDFLGMAAAHMPFLCNHLFLVPVGEEE

Parental  NANPTHRLLCYLLHLRFRSSRSGRLSLHGDIRLLFSRRSLELDTGLPYELQAVTEAPHNPRYSPLP
          NAN.TH.LLCY.LHLRF..S..G.LSL..D..LLFS..SLELDTGLPYELQAVTEAP.NPRY.PLP
Retrocopy NANSTHCLLCYSLHLRFQNSHLGLLSLNRDLHLLFSH*SLELDTGLPYELQAVTEAPPNPRY*PLP

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	0.04 RPM	10.89 RPM
SRP051959_heart	0.00 RPM	5.95 RPM
SRP051959_kidney	0.00 RPM	5.24 RPM
SRP051959_liver	0.00 RPM	1.82 RPM
SRP051959_lung	0.03 RPM	9.58 RPM
SRP051959_lymph_node	0.07 RPM	3.47 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.55 RPM
SRP051959_spleen	0.02 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1357 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1357 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009210	1 retrocopy	retro_cjac_1357 ,
Homo sapiens	ENSG00000005238	1 retrocopy	retro_hsap_2831,
Gorilla gorilla	ENSGGOG00000003218	1 retrocopy	retro_ggor_1966,
Microcebus murinus	ENSMICG00000005528	1 retrocopy	retro_mmur_1580,
Macaca mulatta	ENSMMUG00000011862	1 retrocopy	retro_mmul_1504,
Nomascus leucogenys	ENSNLEG00000004530	1 retrocopy	retro_nleu_1207,
Pongo abelii	ENSPPYG00000019101	1 retrocopy	retro_pabe_2200,
Pan troglodytes	ENSPTRG00000020904	1 retrocopy	retro_ptro_1919,