RetrogeneDB ID: retro_cfam_2054

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:31930478..31930848(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1A
• Ensembl ID: ENSCAFG00000008735
• Aliases: None
• Description: MOB kinase activator 1A [Source:HGNC Symbol;Acc:16015]

Sequence

>retro_cfam_2054
ACCAGGTCAGAACTCTGCACTGAAGCAAGCTGTCTAGTCACAACTGCAGGTCCCAGATCCGAATATCGTTGGGAAGATGC
TATTAATTTTAAGGCCCAGTCAAAGGTTCTACTCCAAAATACATCAACTGTTTGATGACTTGAGTTCAGGATTAATTGGT
CATGAAACCCTTTTTCCTTCTTAAGATTGGTGTCCCATTTTCCCAAAACTTTTTATCTGTGGTAAGGACTATTCTAAAGC
ATTCGTTTAAGGTTTATGCCCATATTTCTTGACAGCACTTTGATTCTGTGATGCAAGAACAAGAAAAGGCCTGCCACAAC
ACATCCTTTAAGTATTTTATTTGTTCTAAAGTTCGATTTCATTGATAGAT

Alignment

ORF - retro_cfam_2054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 57.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TITEFCTEASCPVMSAGPRYEYHWADGTNIKK-PIKCSAPKYIDYLMTWVQDQL-DDETLFPS-KIGVPF
          T..E.CTEASC.V..AGPR.EY.W.D..N.K..P.K.S.PKYI..LMT.VQD.L...ETLFPS.KIGVPF
Retrocopy TRSELCTEASCLVTTAGPRSEYRWEDAINFKA<PVKGSTPKYINCLMT*VQD*L<GHETLFPS>KIGVPF

Parental  PKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFKHFI-FFVQEFNLID
          ..NF.SV..TILK..F.VYAHI..QHFDSVMQ.QE.A..NTSFK.FI..F.....LID
Retrocopy SQNFLSVVRTILKHSFKVYAHIS*QHFDSVMQEQEKACHNTSFKYFI<LF*SSISLID

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	12.77 RPM
SRP017611_brain	0.00 RPM	7.94 RPM
SRP017611_kidney	0.00 RPM	19.08 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2054 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2054 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017359	1 retrocopy	retro_amel_1889,
Canis familiaris	ENSCAFG00000008735	1 retrocopy	retro_cfam_2054 ,
Dasypus novemcinctus	ENSDNOG00000012838	3 retrocopies	retro_dnov_1948, retro_dnov_2226, retro_dnov_337,
Echinops telfairi	ENSETEG00000018245	1 retrocopy	retro_etel_425,
Macaca mulatta	ENSMMUG00000015208	2 retrocopies	retro_mmul_1299, retro_mmul_297,
Mustela putorius furo	ENSMPUG00000007824	2 retrocopies	retro_mputfur_754, retro_mputfur_770,
Otolemur garnettii	ENSOGAG00000003504	1 retrocopy	retro_ogar_2688,
Rattus norvegicus	ENSRNOG00000042657	2 retrocopies	retro_rnor_2544, retro_rnor_2545,