RetrogeneDB ID: retro_cfam_1902

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:18280619..18281313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIM
• Ensembl ID: ENSCAFG00000004529
• Aliases: None
• Description: vimentin [Source:HGNC Symbol;Acc:12692]

Sequence

>retro_cfam_1902
AAGGTGAGGAGCAGTGTGCCTGGCATGCGTCTGGTGCAGGACTCAGTATAGTTCTCACTGGCTGAAACTATCAACACCGA
GTTCAAGAACACTTGCACTGGGAAAGTGGAGCTGCAGGAGCTCAATGACCGCTTTGCTAACTACATCAAGGTGTGCTTCC
TGGAGCAGCAGAACAAGATCCTGCTGAGTGAACTCAAGCAGCTCAAGGGCCTGGGCAAATTGGGCCTGGGGGACCTCTAT
GAGAAGAAGATGTGAGGGCTGTGCCAGCAGGTAGGCCAGCTCACCAAGAACAAGGCCTATGTCAAAGGGAGCAGGACACC
TGGCTGAAGGCATCATGTGGCTCTAGGAGAAGTTGCAGGAGGAGATGCTTCAAGGAGAGGAAGCCTAGAGCACCCTGCAG
TCTTTCAGGCAGAATGTTGACAATACTTCTTTGGCATGTCTTGACCTTGAGTGTGAAGTGGAATCCTTGCAAGAAGAGAT
TGCCTTTTTGAAGAAACTATATGATGAGGAAATCCAGGAGCTTCAGGTCCAGATTCAGGACCAGCATGCCCAAATCCGTA
TTGATGTTTCCAAGCCTGACCTCATGGCTGCCCTCCATGATGTGCCCTGGCAGTATGAAAACATGGCTACCAAGAACCTT
CAGGAGGCCAAGGAATGGTACAAGTCCAAATCTGCCAACCTCTCTGAGGCTGCT

Alignment

ORF - retro_cfam_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.42 %
• Parental protein coverage: 50.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLRSSVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL
          ..RSSVPG.RL.QDSV.FSLA..INTEFKNT.T..KVELQELNDRFANYI.KV.FLEQQNKILL.EL.QL
Retrocopy KVRSSVPGMRLVQDSV*FSLAETINTEFKNTCTG-KVELQELNDRFANYI-KVCFLEQQNKILLSELKQL

Parental  KGQGKSRLGDLYEEEMRELRRQVDQLTNDKARV-EVERD-NLAEDIMRLREKLQEEMLQREEAESTLQSF
          KG.GK..LGDLYE..M..L..QV.QLT..KA.V...E.D..LAE.IM.L.EKLQEEMLQ.EEA.STLQSF
Retrocopy KGLGKLGLGDLYEKKM*GLCQQVGQLTKNKAYV<QREQD<HLAEGIMWL*EKLQEEMLQGEEA*STLQSF

Parental  RQDVDNASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKPDLTAALRDVRQQY
          RQ.VDN.SLA.LDLE..VESLQEEIAFLKKL.DEEIQELQ.QIQDQH.QI..DVSKPDL.AAL.DV..QY
Retrocopy RQNVDNTSLACLDLECEVESLQEEIAFLKKLYDEEIQELQVQIQDQHAQIRIDVSKPDLMAALHDVPWQY

Parental  ESVAAKNLQEAEEWYKSKFADLSEAA
          E..A.KNLQEA.EWYKSK.A.LSEAA
Retrocopy ENMATKNLQEAKEWYKSKSANLSEAA

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
SRP012049_cerebellum	0.00 RPM	192.48 RPM
SRP017611_brain	0.00 RPM	84.31 RPM
SRP017611_kidney	0.07 RPM	172.09 RPM
SRP017611_liver	0.22 RPM	104.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1902 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1902 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004529	2 retrocopies	retro_cfam_1902 , retro_cfam_2022,
Dasypus novemcinctus	ENSDNOG00000011305	1 retrocopy	retro_dnov_72,