RetrogeneDB ID: retro_cfam_1147

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:25415797..25416088(-)
• Located in intron of: ENSCAFG00000008573

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSCAFG00000004215
• Aliases: None
• Description: methionine sulfoxide reductase B2 [Source:HGNC Symbol;Acc:17061]

Sequence

>retro_cfam_1147
GACACAGGGAATCTTACACAGTGTGAGCCATCACTTGCCGCAAGTGAGTGACAAAAGAAATCAACTCCAGAACAAATTCT
ATGTTATGAGAGAGAAAGGAAAGGAACTGCCTTTCAGTGGGATCAACCTGCATAACATGGAGTCAGGCAAGTATGCTGTG
TGTGCTATGACAGCTACTCTTCTGTGAGCAAGTACTGCTCTGGCACTGGATGGCCTTCCTTTTCTGAGACTCACAGGATG
TCTGGCTCTGATAAAAGTAGCACAGGGATGCTGAGATGTGTGGACACCTCA

Alignment

ORF - retro_cfam_1147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 55.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DAGSLTKHELPLTKSEWQKKLTPEQ-FYVTREKGTEPPFSGVYLNNKESGMYH-CVCCDSPLFSSEKKYC
          D.G.LT..E..L..SE.QKK.TPEQ.FYV.REKG.E.PFSG..L.N.ESG.Y..CVC.DS...SS..KYC
Retrocopy DTGNLTQCEPSLAASE*QKKSTPEQ>FYVMREKGKELPFSGINLHNMESGKYA<CVCYDS--YSSVSKYC

Parental  SGTGWPAFSEAHGTSGSDERDTGILRRVDTS
          SGTGWP.FSE.H..SGSD...TG.LR.VDTS
Retrocopy SGTGWPSFSETHRMSGSDKSSTGMLRCVDTS

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	12.10 RPM
SRP017611_brain	0.00 RPM	34.30 RPM
SRP017611_kidney	0.00 RPM	51.11 RPM
SRP017611_liver	0.00 RPM	9.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1147 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1147 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_593

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147 ,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218,