RetrogeneDB ID: retro_cfam_1289

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:14913447..14913802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD6
• Ensembl ID: ENSCAFG00000011044
• Aliases: None
• Description: programmed cell death 6 [Source:HGNC Symbol;Acc:8765]

Sequence

>retro_cfam_1289
ATGTTTGACTGAGAGAACAAGGCTGGCATGAACTTCAGCAAGTCCAATGGCATCTGGAGGTCCATCACAGACTGCAGAAC
ATCTTTCACACCTATGACAGGGGCAATTCTGAGATGATTAACAAGAACGAGCTCAAGCAAGCACTCTCAGGGTACTGGCT
CTCTGACCAGTCTCATGACATTCTCATTTGAAAGTTGGACAGACAAGTATGGGAGCAGATCAGATTTGATGACTTCATCC
AGGGATGCATCCTCTTGCAGGCATTGACAGATATGCACAGGTGTTATGATGGGGATCAGGATGACTGAATTCGGTGTCAT
ATGAACAGTATCTGTCCATGGTCTTCAGCATTGTA

Alignment

ORF - retro_cfam_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.54 %
• Parental protein coverage: 64.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFDRENKAGVNFSEFTGVWKYITDW-QNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFD
          MFD.ENKAG.NFS...G.W..ITD..QN.F.TYDR.NS.MI.KNELKQALSG..Y.LSDQ.HDILI.K.D
Retrocopy MFD*ENKAGMNFSKSNGIWRSITDC<QNIFHTYDRGNSEMINKNELKQALSG--YWLSDQSHDILI*KLD

Parental  RQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQ-VSYEQYLSMVFSIV
          RQ...QI.FDDFIQGCI.LQ.LTD..R.YD.DQD..I..VSYEQYLSMVFSIV
Retrocopy RQVWEQIRFDDFIQGCILLQALTDMHRCYDGDQDD*IR<VSYEQYLSMVFSIV

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	27.34 RPM
SRP017611_brain	0.00 RPM	33.27 RPM
SRP017611_kidney	0.00 RPM	52.04 RPM
SRP017611_liver	0.00 RPM	9.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1289 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008464	1 retrocopy	retro_amel_498,
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Canis familiaris	ENSCAFG00000011044	2 retrocopies	retro_cfam_1289 , retro_cfam_1695,
Felis catus	ENSFCAG00000025521	1 retrocopy	retro_fcat_1800,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840,