RetrogeneDB ID: retro_cfam_429

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:52990350..52990815(+)
• Located in intron of: ENSCAFG00000002334

Retrocopy information

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

Parental gene information

• Parental gene symbol: IRAK1BP1
• Ensembl ID: ENSCAFG00000002793
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 1 binding protein 1 [Source:HGNC Symbol;Acc:17368]

Sequence

>retro_cfam_429
TGCTGCTACCTGGACTACATCACACAGAACCTCCAGCAGCAGTGTCTGCAGACAGAAAATGTACCTGTGACAAAGGGTTT
TAGGAGAGTGGAAAATGCTTATCATGTGGAAGCAGAGCTCTGCAGTACATTTACTGAATTTAGAAAAATGCAAAATATTT
GTAACTTTCTTGTTGAAAAGCTAGATAGCTCTGTTGTCATCAGCCAACCCCAGTTCTGTTATACTCCAGGTTCTGTTGAG
AATCTAAGATGGCAAGCTTGTTTTGTTGTGAACGTGTGATGCAAAGCTCAAGTCTATAACCTTATTGACCAAATTCTGGG
AAAGTCTTTATTCATCAAAAAAAGAAACAAAAGAATGGGAAGGCTGAATAGATGATCCCAGTCATCCAGATTCTCAAGTT
CATTAACTGTACAACAAAAAAATCACAGTGCAAAAATATATGCTGCTTCAAAAGTATTTATAACT

Alignment

ORF - retro_cfam_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 61.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRRLDYITQSLRQQGLQAENVTVTKDFRRVENAYHMEAEVCITFTEFGKMQNICNFLVEKLDSSVVISQP
          C..LDYITQ.L.QQ.LQ.ENV.VTK.FRRVENAYH.EAE.C.TFTEF.KMQNICNFLVEKLDSSVVISQP
Retrocopy CCYLDYITQNLQQQCLQTENVPVTKGFRRVENAYHVEAELCSTFTEFRKMQNICNFLVEKLDSSVVISQP

Parental  QFYHTPGSVENLRRQACLVAVENAWRKAQEVCNLVGQTLGKPLLIKEEETKEWEGQIDDLQSSRLSSS-L
          QF..TPGSVENLR.QAC.V...N...KAQ.V.NL..Q.LGK.L.IK........G.......S...SS.L
Retrocopy QFCYTPGSVENLRWQACFVV--NV*CKAQ-VYNLIDQILGKSLFIKKRNKR--MGRLNR*SQSSRFSSSL

Parental  TVQQKIKSATIHAASKVFIT
          TVQQK..SA.I.AASKVFIT
Retrocopy TVQQKNHSAKIYAASKVFIT

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	15.04 RPM
SRP017611_brain	0.00 RPM	10.32 RPM
SRP017611_kidney	0.00 RPM	9.11 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_429 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_429 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
Ailuropoda melanoleuca	ENSAMEG00000012945	1 retrocopy	retro_amel_783,
Canis familiaris	ENSCAFG00000002793	1 retrocopy	retro_cfam_429 ,
Monodelphis domestica	ENSMODG00000018444	1 retrocopy	retro_mdom_1885,
Oryctolagus cuniculus	ENSOCUG00000001488	1 retrocopy	retro_ocun_347,