RetrogeneDB ID: retro_cjac_2048

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:34992966..34994584(-)
• Located in intron of: ENSCJAG00000008881

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE3A
• Ensembl ID: ENSCJAG00000003764
• Aliases: None
• Description: None

Sequence

>retro_cjac_2048
GAGAAAGAGGATTATTCCCTTTTAATCTGAGTTATTGGAAGAGTTTTTTCTAGTGCTGAGGCATTGGTACAGAGGTTCTG
GAAAGTTACACAACATACCAAGGAAGAACTGAAATCTCTTCAAGCAAAGGATGAAGACAGGGATGAAGATGAAAAGGAAA
AATCTGCATGTTCTCCTCCTGCTATGGAAGAAGACTCAGAAGCATCTTCCTCAAGGGTAGGTGATGGCTCACAGGGAGAC
AACAGTTTGCAAATATTAGGCCCTGATGATGTGTCTGTGGATATTGATGCCATTAGAGGGGTCTACACCAGATTGCTCTC
TAATGAAAAAATTGAAACTGCCTTTCTCAGTGCACTTGTATATTTGTTACCTAACGTGGAATGTGACTTGATGTATCACA
ATGTATGCTCTTGAGATCCTAATTATCTGCATTTGTTCATTATCGTAGTGGAGAATAGAAATCTCCACAGTCCCGAATAT
CTGGAAATGGCTTTGCCATTATTTTGCAAAACAGTGAGCAAGCTACCCCTTGCAGCCCAAGGAAAACTGATCAGACTGTT
GGTCTAAATACAATGCAGACCAGCTTCGGAGAATGATGGAGACATTTCAGCGATTTATTACTTATGAAGTCTTGAGCAAT
GAATTTAACAGTTGAAATCTAGTGAATGATGATGATGCCATTATTGCTGCTTCCAAGTGCTTGAAAACGGTTTACTATAC
AAATGTAGTGGGAGGAGAAGCGGACACAAATCACACTGAAGAAGATGATGAAGAGCCCATCCCTGAGTCCAGTGAGCTGA
CACTTCAGGAACTTTTGGGAAAAGAAAGAAGAAAGAAAGGTTCTTGAGACACCCTGGAAACTGAACTTGGTGTTAAAACC
TTGGATTGTCAGAAACTACGTATCCTCTTTTGAAGAGTTTATTAATGAACCACTGCATGAGGTTCTAGAAATGGATAAAG
ATTATACTGTTTTTTAAAAGTAGAAACAAATTATCTTCTATGATGTGTCCCTTTGTACTGTATGCTGTCACAAAGACTTT
GGGATTGTATAATGACAGAAGTTGCATGTACAGTGAATGAAGAATCACTGTTCTCGACAGCTTAGTTCAAGGACAGCAGT
TGAATCCATATTTGAGACTCAGAGTTAGATGTGACCATATCATAGGTGATGCACTTGTCCAGCTAGAGATGATTGCTGTG
GAAAATCCTGCAGACTTGAAGAAGCAGTTGTTTGTGGAATTTGAAGGAGAACAAGGAGTTGATGAGGGAGATGTTTCCAA
AGAATTTTCTCGGTTGGTTGTGGAGGAAATCTGCAGTCCAGATATTGGTATGTTCACATAAGAAGAATCGACAAAATTGT
TTTGGTTTAATCCATCTTCTTTTGAAACTGAGGGTCAGTTTACCCTGATTGGCACAGTACCAAGTCTGACTATTTGCAAC
AACTGTATACTGGATGTACATTTTCCAATAATTGTCTACAGAAAGCTAATGGGGAAAAAAGGGACTTTTTGTGACTTGGT
AGACTCTTACCAAGTTCTATATCAGACTTTAAAAGATTTATTGGAGTATGAAGGGGATAAAAGATGACATGATGATCATT
TTCCAGATATCACTGACA

Alignment

ORF - retro_cjac_2048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 62.1 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EREDYSPLIRVIGRVFSSAEALVQSFRKVKQHTKEELKSLQAKDEDKDEDEKEKAACSAAAMEEDAEASS
          E.EDYS.LI.VIGRVFSSAEALVQ.F.KV.QHTKEELKSLQAKDED.DEDEKEK.ACS..AMEED.EASS
Retrocopy EKEDYSLLI*VIGRVFSSAEALVQRFWKVTQHTKEELKSLQAKDEDRDEDEKEKSACSPPAMEEDSEASS

Parental  SRIGDTSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNVYSRDP
          SR.GD.SQGDN.LQ.LGPDDVSVDIDAIR.VYTRLLSNEKIETAFL.ALVYL.PNVECDL.YHNV.S.DP
Retrocopy SRVGDGSQGDNSLQILGPDDVSVDIDAIRGVYTRLLSNEKIETAFLSALVYLLPNVECDLMYHNVCS*DP

Parental  NYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRL-WSKYNADQIRRMMETFQQLITYK
          NYL.LFIIV.ENRNLHSPEYLEMALPLFCK..SKLPLAAQGKLIRL.WSKYNADQ.RRMMETFQ..ITY.
Retrocopy NYLHLFIIVVENRNLHSPEYLEMALPLFCKTVSKLPLAAQGKLIRL>WSKYNADQLRRMMETFQRFITYE

Parental  VISNEFNSRNLVNDDDAIVAASKCLKMVYYANVVGGEVDTDHNEEDDEEPIPESSELTLQELLGEERRNK
          V.SNEFNS.NLVNDDDAI.AASKCLK.VYY.NVVGGE.DT.H.EEDDEEPIPESSELTLQELLG.ERR.K
Retrocopy VLSNEFNS*NLVNDDDAIIAASKCLKTVYYTNVVGGEADTNHTEEDDEEPIPESSELTLQELLGKERR-K

Parental  KGPRVDPLETELGVKTLDCRKPLI-PFEEFINEPLNEVLEMDKDYT-FFKVETENKFSFMTCPFILNAVT
          KG...D.LETELGVKTLDC.K..I..FEEFINEPL.EVLEMDKDYT.FFK....NK.S.M.CPF.L.AVT
Retrocopy KG-S*DTLETELGVKTLDCQKLRI>SFEEFINEPLHEVLEMDKDYT>FFK--SRNKLSSMMCPFVLYAVT

Parental  KNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDALVRLEMIAMENPADLKKQLYVE
          K.LGLY.D.R..MYSE.RITVL.SLVQGQQLNPYLRL.VR.DHII.DALV.LEMIA.ENPADLKKQL.VE
Retrocopy KTLGLYND-RSCMYSE*RITVLDSLVQGQQLNPYLRLRVRCDHIIGDALVQLEMIAVENPADLKKQLFVE

Parental  FEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFWFNPSSFETEGQFTLIGIVLGLAIYNNCI
          FEGEQGVDEG.VSKEF..LVVEEI..PDIGMFT..ESTKLFWFNPSSFETEGQFTLIG.V..L.I.NNCI
Retrocopy FEGEQGVDEGDVSKEFSRLVVEEICSPDIGMFT*EESTKLFWFNPSSFETEGQFTLIGTVPSLTICNNCI

Parental  LDVHFPMVVYRKLMGKKGTFRDLGDSHPVLYQSLKDLLEYEGN-VEDDMMITFQISQT
          LDVHFP..VYRKLMGKKGTF.DL.DS..VLYQ.LKDLLEYEG....D.M.I.FQIS.T
Retrocopy LDVHFPIIVYRKLMGKKGTFCDLVDSYQVLYQTLKDLLEYEGD>KDDMMII-FQISLT

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	0.02 RPM	55.69 RPM
SRP051959_heart	0.00 RPM	75.91 RPM
SRP051959_kidney	0.04 RPM	67.11 RPM
SRP051959_liver	0.00 RPM	53.42 RPM
SRP051959_lung	0.00 RPM	64.89 RPM
SRP051959_lymph_node	0.02 RPM	61.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	86.83 RPM
SRP051959_spleen	0.02 RPM	61.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2048 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2048 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003764	1 retrocopy	retro_cjac_2048 ,
Homo sapiens	ENSG00000114062	1 retrocopy	retro_hsap_2523,
Gorilla gorilla	ENSGGOG00000003955	1 retrocopy	retro_ggor_1575,
Pongo abelii	ENSPPYG00000006272	1 retrocopy	retro_pabe_1855,
Pan troglodytes	ENSPTRG00000006829	1 retrocopy	retro_ptro_1468,