RetrogeneDB ID: retro_cfam_662

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:38845607..38846075(+)
• Located in intron of: ENSCAFG00000006596

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000014614
• Aliases: None
• Description: None

Sequence

>retro_cfam_662
TCTGCACTCATTGCCAGAGGGGCCATGGATACTCTGGAAACTTGACAGACACAGATTAGGAACATCCAACAGTGAGATTC
ATCACTGACCTGGAAATTCATTCCCATGAGATCAGAACCTCTACAAAAGAAGGTACATTCTGAAAAAGACTAAGCAGTGA
AGGACCATTTGAAAAAGAAGGTCTGTTGGTTGGAAAAGGCTGGAGAGCTAATTTCCACTGAAGATTTTATCACCCCTGTG
AAGTTCTTGGATAAAGTAAGACAGCGGCCTCGGGTAGAGCTCCCTTTTGAGAAGAGTCAGAGGAGACCTCTGCTTCTGAA
AACATAGTCCTGGTAGAAGCAGCAAGAGCACAAAATGGAGAAGGATGCCATGAGATCTGTGTTTGAGGCTCAACAGGAAG
CTCTGTTGGAGCTGTGACTCATATCCTAGGGGCTCCATGTGAAGGCCATCAAGCAGGATCCCAGTTTA

Alignment

ORF - retro_cfam_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.5 %
• Parental protein coverage: 77.67 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SARALRSRSGLLGPWQTQMRETHQRAALLSFWELIPMRAEPLRKKKKVDPKKDQAVKDRLKKRIRRLEKA
          SA...R.....L...QTQ.R...Q....L..W..IPMR.EPL.KK..V...KD.AVKD.LKK....LEKA
Retrocopy SALIARGAMDTLET*QTQIRNIQQ*DSSLT-WKFIPMRSEPLQKK--VHSEKD*AVKDHLKKKVCWLEKA

Parental  SQELIPIEDFITPVKLLDKTRQRPKVELPFEESERRALLLKKWSLYKHQEHEKERDAITSMLESQQEALE
          ..ELI..EDFITPVK.LDK.RQRP.VELPFE.S.RR.LLLK..S..K.QEH..E.DA..S..E.QQEAL.
Retrocopy G-ELISTEDFITPVKFLDKVRQRPRVELPFEKSQRRPLLLKT*SW*KQQEHKMEKDAMRSVFEAQQEALL

Parental  ELKLISPELHEEATKRDPNL
          EL.LIS..LH..A.K.DP.L
Retrocopy EL*LIS*GLHVKAIKQDPSL

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	27.64 RPM
SRP017611_brain	0.00 RPM	17.55 RPM
SRP017611_kidney	0.00 RPM	75.08 RPM
SRP017611_liver	0.00 RPM	15.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_662 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_662 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_687

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014614	2 retrocopies	retro_cfam_1686, retro_cfam_662 ,