RetrogeneDB ID: retro_cjac_1456

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:26079012..26079945(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1456
ACCAGGTCTGTGTCCTCATCCTCCTACCGCAGGATGTTCGGCAGCCCAGGCACCGCGAGCCAGCCGAGCTCTAGCCAGAG
CTATGTGACCACTTCCACCCACACCCACAGCCTGGGCAGCTCGCTGCGCCCCAGCACCAGCCACAGCCTCTATGCCTCAT
CCCCGGGCGGCGTGTATGCCATGCGCTCCTCGGCAGTGCGCCTGCGGAGCAGCGTGCCCGGGGTGCGACTGCTGCAGGAC
TCGATGGACTTCTCGCTGGCCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAACGAGAAGGTGGAGCTGCAGGA
GCTGAACGACCGCTTCGCAAACTACATCGACAAGGTGCGCTTCCTGGAGCAGCAGAATAAGATCCTGCTGGCCGAGCTCG
AGCAGCTCAAGGGCCAGAGCAAGTCGCGCCTGGGGGACCTCTACGAGGAGGAGATGCGGAAGCTGCGCCGGCAGGTGGAC
CAGCTCACCAACGACAAAGCCCGCGTCTAGGTGGAACGCGACAACCTGGCCGAGGACATCATGCACCTCCGGGAGAAATT
GCAGGAGGAGATGCTTCAGAGAAAGGAAGCCGAGAGCACCCTGCAATCTTTCAGACAGGATGTTAACAATACGTCTCCGG
CACGTCTTGACCTTGAACGCAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAAATACACGAAGAGGAAATC
CAGGAGCTGCAGGCTCAGATTCAGGAACAGCATGTCCAGATCGATGTGAACGTTTCCAAGCCGGACCTCACGGCTGCCCT
GCGTGACGTATGTCAGCAGTATGAAAGTGTGGCTGCCAAGAACCTGCAGGAGGCAGAAGAATGGTACAAGTCTAAGTTTG
TTGACCTCTCCGAGGCTGCCAACCCAATGATGCCCTACGCCAGGCAAAGCAGG

Alignment

ORF - retro_cjac_1456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91. %
• Parental protein coverage: 66.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TRSVSSSSYRRMFGGPGTASRPSSSRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGVYATRSSAVRLRS
          TRSVSSSSYRRMFG.PGTAS.PSSS.SYVTTST.T.SLGS.LRPSTS.SLYASSPGGVYA.RSSAVRLRS
Retrocopy TRSVSSSSYRRMFGSPGTASQPSSSQSYVTTSTHTHSLGSSLRPSTSHSLYASSPGGVYAMRSSAVRLRS

Parental  SVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQLKGQG
          SVPGVRLLQDS.DFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQLKGQ.
Retrocopy SVPGVRLLQDSMDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQLKGQS

Parental  KSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAESTLQSFRQDVDN
          KSRLGDLYEEEMR.LRRQVDQLTNDKARV.VERDNLAEDIM.LREKLQEEMLQR.EAESTLQSFRQDV.N
Retrocopy KSRLGDLYEEEMRKLRRQVDQLTNDKARV*VERDNLAEDIMHLREKLQEEMLQRKEAESTLQSFRQDVNN

Parental  ASLARLDLERKVESLQEEIAFLKKIHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAK
          .S.ARLDLERKVESLQEEIAFLKKIHEEEIQELQAQIQEQHVQIDV.VSKPDLTAALRDV.QQYESVAAK
Retrocopy TSPARLDLERKVESLQEEIAFLKKIHEEEIQELQAQIQEQHVQIDVNVSKPDLTAALRDVCQQYESVAAK

Parental  NLQEAEEWYKSKFADLSEAANRNNDALRQAK
          NLQEAEEWYKSKF.DLSEAAN......RQ..
Retrocopy NLQEAEEWYKSKFVDLSEAANPMMPYARQSR

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	0.35 RPM	195.54 RPM
SRP051959_kidney	0.04 RPM	80.47 RPM
SRP051959_liver	0.09 RPM	7.82 RPM
SRP051959_lung	0.33 RPM	193.79 RPM
SRP051959_lymph_node	0.16 RPM	145.22 RPM
SRP051959_skeletal_muscle	0.17 RPM	66.47 RPM
SRP051959_spleen	0.29 RPM	110.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1456 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1456 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1456 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,