RetrogeneDB ID: retro_cfam_1341

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:38967849..38968450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010399
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBR4
• Ensembl ID: ENSCAFG00000007520
• Aliases: None
• Description: carbonyl reductase 4 [Source:HGNC Symbol;Acc:25891]

Sequence

>retro_cfam_1341
AGGGCAGTGACCCAATTAATGGCCCAGAAGGGCTACTGATTGGCCATCATCCTCAGAAGTCTGCAAGTGGCCAAAGCCAC
TGGTGCTGGTGACTGTGGTGGAGATCATTTGGCATTTAGCTATGATGCTGCCAAAAGACATAAGGCTCAAAATACATTTG
AAGAGATGGAGAAAAATTTAGGTCGACTTTATCTCTTAGTAAATGCAGCTGGAATTAATAGGGATAGCCTTTTAGTAAGA
ACAAAAGCTGAAGATAAGATATCTTGGCACATACTAACCTGATGGTTCTGTGCTGACTTGGAAAGCTGCCAGAAAGGCTA
TGATTCAACACCAAAGAGGATCTATTGTTACTAGAGGACATACTGGTTTCAAAGGCAATTCTGGCCAATCTTTGTATAGC
GTCAGTAAAGGAAGATGCATTAAATTTGCATATACTTTTGCTAAAGAAGTTACAAGAAAGAAAATTGCAGTGAATGTAGT
TGTACCAGTATTTGTCCACACGGATAGGACGAAAGACTTGAACATGTAAAGAAAAATACCTCTCTTGGGAGGTTTGGAGA
ACCTATCGATGTGCACATTTTTCCTTTGAGAATCGCCATAT

Alignment

ORF - retro_cfam_1341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 86.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAVAQVMAQKGYRLAVIARNLEGARAA-AGELGGDHLAFSCDVAKERDVQNTFEEMEKNLGRVNFLVNAA
          RAV.Q.MAQKGY.LA.I.R.L..A.A..AG..GGDHLAFS.D.AK....QNTFEEMEKNLGR...LVNAA
Retrocopy RAVTQLMAQKGY*LAIILRSLQVAKATGAGDCGGDHLAFSYDAAKRHKAQNTFEEMEKNLGRLYLLVNAA

Parental  GINRDSLLVRTKTEDMIS-QLHTNLL-GSMLTCKAALKTMIQQQRGSIVNVGSIIGLKGNSGQSVYSASK
          GINRDSLLVRTK.ED.IS...HTNL..GS.LT.KAA.K.MIQ.QRGSIV..G...G.KGNSGQS.YS.SK
Retrocopy GINRDSLLVRTKAEDKIS<LAHTNLM<GSVLTWKAARKAMIQHQRGSIVTRGH-TGFKGNSGQSLYSVSK

Parental  GGLVGFSRALAKEVARKKIRVNVVAPGFVHTDMTKDLKEEHLKKNIPLGRFGEPIDVAHAVVFLLESPY
          G....F....AKEV.RKKI.VNVV.P.FVHTD.TKDL........IPL...G..........FL.ESPY
Retrocopy GRCIKFAYTFAKEVTRKKIAVNVVVPVFVHTDRTKDL---NM*RKIPL--LGGLENLSMCTFFL*ESPY

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	4.37 RPM
SRP017611_brain	0.00 RPM	3.57 RPM
SRP017611_kidney	0.00 RPM	13.08 RPM
SRP017611_liver	0.00 RPM	7.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1341 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1341 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013400	1 retrocopy	retro_amel_1352,
Canis familiaris	ENSCAFG00000005927	1 retrocopy	retro_cfam_2172,
Canis familiaris	ENSCAFG00000007520	1 retrocopy	retro_cfam_1341 ,
Canis familiaris	ENSCAFG00000014368	4 retrocopies	retro_cfam_1199, retro_cfam_1212, retro_cfam_1273, retro_cfam_568,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Felis catus	ENSFCAG00000030280	1 retrocopy	retro_fcat_885,
Oryctolagus cuniculus	ENSOCUG00000006446	1 retrocopy	retro_ocun_1883,
Tursiops truncatus	ENSTTRG00000000258	1 retrocopy	retro_ttru_1855,