RetrogeneDB ID: retro_cjac_3599

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01187446.1:625..1625(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3KBP1
• Ensembl ID: ENSCJAG00000005449
• Aliases: None
• Description: SH3-domain kinase binding protein 1 [Source:HGNC Symbol;Acc:13867]

Sequence

>retro_cjac_3599
GTTCTCAGTGGGAAGACTGGAATGTTTCCTTCCAACTTCATCAAGGAGTTTTTGGGGTAGTCAGATAAACTTGGCATTTC
CCAGGATGAGCATCTGTCCAAGTCAAGTTTAAGGGAAACCACAGGCTCTGAGAGTGAGGGGGGTGACTCAAGCAGCACCA
AGTCTGAAGGTGTCAATGGGACAGTGGCTACTGCAGCAATCCAGCCCAAAAACGTTAAAGGAGTGGGCTTTGGAGACATT
TTCAAAGACAAGCCAATCAAACTAAGACCAAGATCAATTGAAGCAGAAAATGATTTTCTGAGGGCGGAAAAATCTCTTGG
GAAGAAGTTACCGACAACTCCTGCAACTCCAGACTCCTCAAAAACAGAAATGGACAGCAGGACAAAGCGCAAGGATTTAC
TGCAAAGTGATATTTCCATATGAGGCACAGAATAATGATGAAATGACAATCAAAGAAGGAGATATAGTCACTCTCATCAG
CAAGGACTGCATGAGGTAGGCTGGTGGGAAGGAGAGCTGAATGGAAGATGAGGCGTGTTCCCTGATAACTTAGTGAAGTT
ACTTCCCCCTGACTTTGAAAAGGAAGGGAATAGACCCAAGAAGCCACCGGCTCCATCTGCTCCTGTCATCAAACAAGGGA
CAGGTACCACTGAGAGAAAACATGAACTTAAAAAGATACCTCCTGAAAGACGATAAATGCTTCCCAACAGAACAGAAGAA
AGAGACAGACCAGAGACAGACCCAAAACTGGATTTACAGAAGCCCTCTGTTCCTGTCATACAGCAAAAAAAAGCCTCAGC
CACCTAAGACCAATTCTCTCAGCAGACCTGGTGCACTGCCCCCAAGAAGGCCAGAGCTACCAGTGGGTCCGCTGACACAC
ACCAGGGGTGATTGTCCAAAGATTGACTTGGTGGGCAGTTCATTTTCTGGCATCTTGGACAAAGATCTCTTGGACTGCAG
CAATGACACCGACCTAGAAGGTTTTGACTCTGTGGTATCA

Alignment

ORF - retro_cjac_3599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.31 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLNGKTGMFPSNFIKELSGESDELGISQDEQLSKSSLRETTGSESDGGDSSSTKSEGANGTVATAAIQPK
          VL.GKTGMFPSNFIKE..G.SD.LGISQDE.LSKSSLRETTGSES.GGDSSSTKSEG.NGTVATAAIQPK
Retrocopy VLSGKTGMFPSNFIKEFLG*SDKLGISQDEHLSKSSLRETTGSESEGGDSSSTKSEGVNGTVATAAIQPK

Parental  KVKGVGFGDIFKDKPIKLRPRSIEVENDFLPVEKTIGKKLPATTATPDSSKTEMDSRTKSKD-YCKVIFP
          .VKGVGFGDIFKDKPIKLRPRSIE.ENDFL..EK..GKKLP.T.ATPDSSKTEMDSRTK.KD.YCKVIFP
Retrocopy NVKGVGFGDIFKDKPIKLRPRSIEAENDFLRAEKSLGKKLPTTPATPDSSKTEMDSRTKRKD>YCKVIFP

Parental  YEAQNDDELTIKEGDIVTLINKDCI-DVGWWEGELNGRRGVFPDNFVKLLPPDFEKEGNRPKKPPPPSAP
          YEAQN.DE.TIKEGDIVTLI.KDC...VGWWEGELNGR.GVFPDN.VKLLPPDFEKEGNRPKKPP.PSAP
Retrocopy YEAQNNDEMTIKEGDIVTLISKDCM<EVGWWEGELNGR*GVFPDNLVKLLPPDFEKEGNRPKKPPAPSAP

Parental  VIKQGAGTTERKHELKKIPPERPEMLPNRTEEKERPEREPKLDLQKPSVPAI-PPKKPRPPKTNSLSRPG
          VIKQG.GTTERKHELKKIPPER..MLPNRTEE..RPE..PKLDLQKPSVP.I...KKP.PPKTNSLSRPG
Retrocopy VIKQGTGTTERKHELKKIPPERR*MLPNRTEERDRPETDPKLDLQKPSVPVI>SKKKPQPPKTNSLSRPG

Parental  ALPPRRPERPVGPLTHTRGDGPKIDLAGSSLSGILDKDLSDRSNDIDLEGFDSVVS
          ALPPRRPE.PVGPLTHTRGD.PKIDL.GSS.SGILDKDL.D.SND.DLEGFDSVVS
Retrocopy ALPPRRPELPVGPLTHTRGDCPKIDLVGSSFSGILDKDLLDCSNDTDLEGFDSVVS

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	4.90 RPM
SRP051959_heart	0.18 RPM	6.75 RPM
SRP051959_kidney	0.13 RPM	7.01 RPM
SRP051959_liver	0.09 RPM	2.58 RPM
SRP051959_lung	0.11 RPM	15.86 RPM
SRP051959_lymph_node	0.16 RPM	23.63 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.47 RPM
SRP051959_spleen	0.08 RPM	15.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3599 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3599 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005449	2 retrocopies	retro_cjac_3599 , retro_cjac_562,