RetrogeneDB ID: retro_cfam_252

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:31046097..31046730(+)
• Located in intron of: ENSCAFG00000000277

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG2
• Ensembl ID: ENSCAFG00000028759
• Aliases: None
• Description: BCL2-associated athanogene 2 [Source:HGNC Symbol;Acc:938]

Sequence

>retro_cfam_252
ATGGCTTAGGCCAAGATCAACACGAAAGCCAATGAGGGGCATTTCTGCTGCTCCTCCTCCATGGCGGACCACTCCAGCCG
CCTGCTGGAGAGCCTGGACAGCTGGAGCTCAGGGTGGAAGCTTTGAGAGAAGCCGCCAACTGCTGTTGAGCAAGAGAAAG
AAATCCTTCTGGAAATGATCCACAGCATCCAGAATAGCCAGGATATGAGGCAGATCAGCGACGGAGAAAGAGAAGAATTA
AATCTGATGGCAAACTGTTTGATGGGATGAACCCTCACTGTTGAAGTTTCAGTAGAAACAATCAGAAACCCCCAGCAGCA
AGAATCCCTAAAGCATGCCACCAGGATTATTGATGAGGTGGTCAGTAAGTTTCTGGATGGTTTGGGAAATGCCAGGAGTC
ACTTGATGTCCCTGTACAGTGCATGTTCATCTGAGGTGCCACCAGGGCCTGTTGACCAGAAGTTTCAGTCCATAGGAATT
GGCTGTGCTCTTGAAGACCAGAAGGAAATTAAGAGAAGATTAGAGACCCTGCTTAGAAATATTGAAAACTCTGACAAGGC
CATCAAGCTGTTAGAGCATTCTAAAGGAGCTGGTTCTAAAACTCTGCAACAAAATACTGAAGGCAAATTTAAT

Alignment

ORF - retro_cfam_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQAKINAKANEGRFCRSSSMADRSSRLLESLD-QLELRVEALREAA-TAVEQEKEILLEMIHSIQNSQD
          MA.AKIN.KANEG.FC.SSSMAD.SSRLLESLD.QLELRVEALREAA.TAVEQEKEILLEMIHSIQNSQD
Retrocopy MA*AKINTKANEGHFCCSSSMADHSSRLLESLD<QLELRVEALREAA>TAVEQEKEILLEMIHSIQNSQD

Parental  MRQISDGEREELNLTANRLMGRTLTVEVSVETIRNPQQQESLKHATRIIDEVVSKFLDDLGNARSHLMSL
          MRQISDGEREELNL.AN.LMG.TLTVEVSVETIRNPQQQESLKHATRIIDEVVSKFLD.LGNARSHLMSL
Retrocopy MRQISDGEREELNLMANCLMG*TLTVEVSVETIRNPQQQESLKHATRIIDEVVSKFLDGLGNARSHLMSL

Parental  YSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETLLRNIENSDKAIKLLEHSKGAGSKTLQQNAEG
          YSACSSEVPPGPVDQKFQSI.IGCALEDQK.IKRRLETLLRNIENSDKAIKLLEHSKGAGSKTLQQN.EG
Retrocopy YSACSSEVPPGPVDQKFQSIGIGCALEDQKEIKRRLETLLRNIENSDKAIKLLEHSKGAGSKTLQQNTEG

Parental  KFN
          KFN
Retrocopy KFN

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	2.90 RPM
SRP017611_brain	0.00 RPM	9.77 RPM
SRP017611_kidney	0.00 RPM	5.55 RPM
SRP017611_liver	0.00 RPM	5.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_252 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028759	1 retrocopy	retro_cfam_252 ,
Myotis lucifugus	ENSMLUG00000004055	1 retrocopy	retro_mluc_251,
Oryctolagus cuniculus	ENSOCUG00000004815	1 retrocopy	retro_ocun_823,
Procavia capensis	ENSPCAG00000011588	1 retrocopy	retro_pcap_295,