RetrogeneDB ID: retro_cjac_1026

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:33495445..33496842(-)
• Located in intron of: ENSCJAG00000013387

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIM
• Ensembl ID: ENSCJAG00000008688
• Aliases: LOC100408168, VIM, vimentin
• Description: vimentin [Source:HGNC Symbol;Acc:12692]

Sequence

>retro_cjac_1026
ATGTCCACTAGGCCAGTGTCCTCGTCCTCCTACCGCAGGATGTTCGGCGGCCAGGGCACCGCAAGCCGGCCAAGCTCCAG
CCGGAGCTACGTGACCACGTCCACCGGCACCTACAGCCTGGGCAGCGCGCTGAGCCCCAGCACCAGCCACAGCCTCTACG
CCTCGTCGCCGGGCGGCGTGTATGCCACGTGCTCCTCAGCAGCGCGCCTACGGAGCAGGGTGCCCGGGGTGCGGCTGCTG
CAGGACTCGGTGGACTTCTCGCTGGCCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAACGAGAAGGTGGAGCT
GCAGGAGCTGAATGACCGCTTCGCAAACTACATCTACAAGGTGCGCTTCCTGGAGCAGCAGAATAAGATCCTGCTGGCCG
AGCTCAAGCAGCTCAAGGGCCAGGGCAAGTCGCGCCTGGGAGACCTCTATGAGGAGGAGATACGGGAGCTGCGCTGGCAG
GTGAACCAGCTCACCAACGACAAAGCCCGCGTCGAGGTGAAGCGCGACAACCTGGCCAAGGACATCATACGCCTCCGGGA
GTAACTGCAGGAGGAGATGCTTCAGAGAGAGGAAGCCGAGAGCACCCTGCAATCTTTCAGACAGGATGTTGACAATGCGT
CTCTGGCACGTCTTGACCTTGAACGCAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAAATACACGAAGAG
GAAATCCAGGAGCTGCAGGCTCAGATTCCGGAACAGCATGTTCAGATCGATGTGGACGTTTCCAAGCCGAACCTCACGGC
TGCCCTGCATGACATACATCAGCAGTATGAAAGTGTGGCTGCCAAGAACCTGCAGGAGGCAGAAGAATGGTACAAGTCTA
AGTTTGCTGACCTCTCCGAGGCTGCCAACCGAAACAATGATGCCCTACGCCAGACAAAGCAGGAGTCCAATGAGTACCGG
ATATAGGTGCAGTCCCTCACCTGTGAAGTGGATGCTCTTAAAGGAACAAACGAGTCCCTGGAAGGCCAGATGCTGAAATG
GAAGAGAATTTTGCCATTGAAGCTGCTAACTACCAAGACACTATTGGCTGCCTGCAGGATGAAATTCAGAACATGAAGGA
TGAAATGACTCCTCACCTTCCTAAATACCAAGACCTGCTCAGTGTTAAGATGGCCCTTGACATTGAGATTGCCACCTACA
GGAAGCTGCTGGAAGGCGAGGAGAGCAGGATTTCTTTGCCTCTTCCAAACTTTTCCTCCCTGAACCTGAGGGAAACTAAT
CTGGATTCACTCCCTCTGGTTGACACACACTCAAAAAGGACACTTCTGATTAAGACGGTTGAAACTAGAGACAGACAGGT
TATCAACAAAACTTCTCAGCATCATGATGATCTTGAA

Alignment

ORF - retro_cjac_1026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTRSVSSSSYRRMFGGPGTASRPSSSRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGVYATRSSAVRL
          MSTR.VSSSSYRRMFGG.GTASRPSSSRSYVTTST.TYSLGSAL.PSTS.SLYASSPGGVYAT.SSA.RL
Retrocopy MSTRPVSSSSYRRMFGGQGTASRPSSSRSYVTTSTGTYSLGSALSPSTSHSLYASSPGGVYATCSSAARL

Parental  RSSVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQLKG
          RS.VPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYI.KVRFLEQQNKILLAEL.QLKG
Retrocopy RSRVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIYKVRFLEQQNKILLAELKQLKG

Parental  QGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAESTLQSFRQDV
          QGKSRLGDLYEEE.RELR.QV.QLTNDKARVEV.RDNLA.DI.RLRE.LQEEMLQREEAESTLQSFRQDV
Retrocopy QGKSRLGDLYEEEIRELRWQVNQLTNDKARVEVKRDNLAKDIIRLRE*LQEEMLQREEAESTLQSFRQDV

Parental  DNASLARLDLERKVESLQEEIAFLKKIHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVA
          DNASLARLDLERKVESLQEEIAFLKKIHEEEIQELQAQI.EQHVQIDVDVSKP.LTAAL.D..QQYESVA
Retrocopy DNASLARLDLERKVESLQEEIAFLKKIHEEEIQELQAQIPEQHVQIDVDVSKPNLTAALHDIHQQYESVA

Parental  AKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEVDALKGTNESLERQM-REMEE
          AKNLQEAEEWYKSKFADLSEAANRNNDALRQ.KQESNEYR..VQSLTCEVDALKGTNESLE.QM..EMEE
Retrocopy AKNLQEAEEWYKSKFADLSEAANRNNDALRQTKQESNEYRI*VQSLTCEVDALKGTNESLEGQM<AEMEE

Parental  NFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFS
          NFA.EAANYQDTIG.LQDEIQNMK.EM..HL..YQDLL.VKMALDIEIATYRKLLEGEESRISLPLPNFS
Retrocopy NFAIEAANYQDTIGCLQDEIQNMKDEMTPHLPKYQDLLSVKMALDIEIATYRKLLEGEESRISLPLPNFS

Parental  SLNLRETNLDSLPLVDTHSKRTLLIKTVETRDGQVINETSQHHDDLE
          SLNLRETNLDSLPLVDTHSKRTLLIKTVETRD.QVIN.TSQHHDDLE
Retrocopy SLNLRETNLDSLPLVDTHSKRTLLIKTVETRDRQVINKTSQHHDDLE

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	0.13 RPM	65.08 RPM
SRP051959_heart	0.65 RPM	195.54 RPM
SRP051959_kidney	0.31 RPM	80.47 RPM
SRP051959_liver	0.00 RPM	7.82 RPM
SRP051959_lung	0.60 RPM	193.79 RPM
SRP051959_lymph_node	0.41 RPM	145.22 RPM
SRP051959_skeletal_muscle	0.15 RPM	66.47 RPM
SRP051959_spleen	0.25 RPM	110.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1026 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1026 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008688	2 retrocopies	retro_cjac_1026 , retro_cjac_1456,
Callithrix jacchus	ENSCJAG00000018178	4 retrocopies	retro_cjac_1685, retro_cjac_394, retro_cjac_4043, retro_cjac_760,
Dasypus novemcinctus	ENSDNOG00000011305	1 retrocopy	retro_dnov_72,
Tarsius syrichta	ENSTSYG00000004937	2 retrocopies	retro_tsyr_1756, retro_tsyr_564,