RetrogeneDB ID: retro_cfam_1138

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:3094315..3095025(-)
• Located in intron of: ENSCAFG00000005270

Retrocopy information

• Ensembl ID: ENSCAFG00000005278
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2R2
• Ensembl ID: ENSCAFG00000031810
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2R 2 [Source:HGNC Symbol;Acc:19907]

Sequence

>retro_cfam_1138
ATGGCCCAGCAGCAGATGACCAGCTCGCAGAAGGCCCTGATTCTCGAGCTGAAATCCCTGCAGGAGGAGCCGGTGGAGGG
CTGCCGGATCACCCTGGTGGATGAGTCCTACCTCTACAACTGGGAGGTTGCCATCTTCAGACCCCCCAACACCCTCTACG
AAGGCGGCTACTTCAAGGCACACATTAAATTTCCTATTGACTACCCATATTCACCACCTACCTTCAGATTCTTGACCAAA
TGTGGCACCCCAACATTTATGAGAATGGAGATGTATGCATTTCGATTCTTCATCCACCTGTAGATGACCCACAGAGTGGA
GAACTGCCCTCTGAAAGGTGGAATCCTACTCAGAATGTCAGGACTATTCTGTTAAATGTAATCTCATTGCTCAATGAGCC
CAACACCTTCTCCCCAGCCAATGTGGATGCTTTGGTTATGTTCAGGAAATGGAGGGACAGTAAAGGAAAAGACAGAGAAT
ATGCTGAAATCATTAGGAAACAGGTTTCAGCCACTAAAGCCGAAGCAGAAAAAGATGGAGTGAAGGTCCCCACTAGCCTG
GTGGAATACTGCATCAAAACTAAAGTGCCTTCCAATGACAACAGCTCAGATTTGCTTTATGACAACTTGTACGAGGGTGA
CATCGATGATGAAGATGAGGAGGAAGATGCCGACTGCTATGATGATGATGATTCTGGGAATGAGGAGTCC

Alignment

ORF - retro_cfam_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPY
          MAQQQMTSSQKAL.LELKSLQEEPVEG.RITLVDES.LYNWEVAIF.PPNTLYEGGYFKAHIKFPIDYPY
Retrocopy MAQQQMTSSQKALILELKSLQEEPVEGCRITLVDESYLYNWEVAIFRPPNTLYEGGYFKAHIKFPIDYPY

Parental  SPPTFRFLTK-MWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSP
          SPPTFRFLTK.MWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILL.VISLLNEPNTFSP
Retrocopy SPPTFRFLTK<MWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLNVISLLNEPNTFSP

Parental  ANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPSNDNSSDLLYDD
          ANVDA.VMFRKWRDSKGKD.EYAEIIRKQVSATKAEAEKDGVKVPT.L.EYCIKTKVPSNDNSSDLLYD.
Retrocopy ANVDALVMFRKWRDSKGKDREYAEIIRKQVSATKAEAEKDGVKVPTSLVEYCIKTKVPSNDNSSDLLYDN

Parental  LYDDDIDDEDEEEEDADCYDDDDSGNEES
          LY..DIDDED.EEEDADCYDDDDSGNEES
Retrocopy LYEGDIDDED-EEEDADCYDDDDSGNEES

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	36.66 RPM
SRP017611_brain	0.00 RPM	26.44 RPM
SRP017611_kidney	0.00 RPM	26.15 RPM
SRP017611_liver	0.00 RPM	24.51 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1138 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138 ,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211, retro_ogar_2040, retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,