RetrogeneDB ID: retro_cfam_2022

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373239.1:626342..627119(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013199
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_2022
GCCACCGGGTCTGTGTCCTCGTCCTCCTACCGCAGGATGTGCGGCGGCCGGCCCGGGAGCCGCCGAGCTCCGCGCGGAGC
TACGCGGCCGCGTCCCCCCGCACCTACAGCCTGGGCGGCGCGCCGCGCCCCGGCACCAGCCGCAGCCTCTAGGCCTCGTC
CCGCGGCGCGTCCGCCACGCGCTCCTCCGCGCTGGCCTGCGGAGCAGTGTGCCTGGCGTGCGTCTGCTGCAGGACTCGGC
GCGCTTCTCGCTGGCCGCCGCCATCAACACCGAGTTCAAGCCCACGCGCACCACGAGAAGCTGCAGCTGCAGGAGCTGAA
TGACTGCTTCGCCAACTGCATCGACAAGGTGCGCTTCCTGGAGCAGCAGAACAGGATCCTGCTGGCCGAGCTCGAGCAGC
TCCGGGGCCAGGGCAAGTCGCGCCTGGGGGACCTCTACGAGGAGGAGCTGCGGGAGCTGCGCCGGCGGGTGGACCAGCTC
ACCAACGACAAGGCCTGCGTCGAGGTGGAGCGCCACGACCCGGTCGAGGACATCATGCGGCTCTGGGAGAAGTTGCAAGA
GGAGATGCTTCAGAGAGAGGAAGCCGAGAGCACCCTGCAGTCTTCCCGACAGGCTGGTGCCAACGCTTCTTTGGCGCGTC
TTGACCTTGAGCGGAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACATGATGAGGAAATCCAGGAG
CTGCAGGCCCAGATTCAGGACCAGCACGTCCAAATCGATATGGATGTTTCCAAGCCA

Alignment

ORF - retro_cfam_2022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 56.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STRSVSSSSYRRMFGGPGTGSR-PSSTRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGAYATRSSAVR-
          .T.SVSSSSYRRM.GG...GSR.PSS.RSY...S.RTYSLG.A.RP.TSRSL.ASS.G.A.ATRSSA...
Retrocopy ATGSVSSSSYRRMCGGR-PGSR<PSSARSYAAASPRTYSLGGAPRPGTSRSL*ASSRG-ASATRSSALA<

Parental  LRSSVPGVRLLQDSVDFSLADAINTEFKNTRT-NEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL
          LRSSVPGVRLLQDS..FSLA.AINTEFK.TRT..EK..LQELND.FAN.IDKVRFLEQQN.ILLAELEQL
Retrocopy LRSSVPGVRLLQDSARFSLAAAINTEFKPTRT<HEKLQLQELNDCFANCIDKVRFLEQQNRILLAELEQL

Parental  KGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAESTLQSFRQ
          .GQGKSRLGDLYEEE.RELRR.VDQLTNDKA.VEVER....EDIMRL.EKLQEEMLQREEAESTLQS.RQ
Retrocopy RGQGKSRLGDLYEEELRELRRRVDQLTNDKACVEVERHDPVEDIMRLWEKLQEEMLQREEAESTLQSSRQ

Parental  DVDNASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP
          ...NASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP
Retrocopy AGANASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP

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	0.07 RPM	104.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2022 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2022 has 0 orthologous retrocopies within eutheria group .

---

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,