RetrogeneDB ID: retro_cfam_1040

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:42704154..42705005(-)
• Located in intron of: ENSCAFG00000009933

Retrocopy information

• Ensembl ID: ENSCAFG00000010023
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSCAFG00000014033
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_cfam_1040
AGCAAGGAGCATGCTGCACCCTTCACGCTCGAGTACCGAGTCTTCCTCAAAAATGAAAAAGAACAATATATATCTCCATT
TCATGATGTTCTGATTTATGCAGATAAGCACATTTTCCACATGGTAGTTGAAGCACCACACTGGTCTAATGCAAAAAAGG
AGATTAGCTACAAAGGACCCTCTAAACCCAATTAAACAAGATGTGAAAAAGGAAAACTCCGTTATGTTGCAAATTTGTTC
CCTTATACAGGATATATCTGCAACTATGGTGCCATCCCCCAGACTTGGGAAGACCCAGGACACAATGACAAACGTACTGG
CTGTTGTGGTGACAATGACCCCATCGATGTGTGTGAAATTGGAAGTAAGGTATGTGCAAGAGGTGAAATACTTAGGGTGA
AAGTTCTGGGCATACTGGCTATGACTGATGAAGGGGAAACCGGCTGGAAAATCATTGCCATTAACGTGGATGATCCTGAT
GCAGCCAATTACAATGATATTTATGATGTCAAGTGGCTGAAACCTGGCTACCTGGAAGCTACTGTGGACTGGTTTAGAAG
GTACAAGATTCCTGGTGGAAAACCAGAGAGTCAGTTTGCTCTCAACGCAGAATTTAAAGATAAGGACTTTGCAACTGATA
TTATTAAAAGCACTCATAATCGTTGGAGAGCATCAGTGATGAAGAAAATCGTGGAAAGGGAATCAGTTGCATGAATACTA
TGGTGTCAGAGAGGCCCTTCAAGTGTGATTCTGATGCTGCCGAAGCTATTGTGGATGCTTTACCACCACCGTGCCAATCT
GCCTGCACGGTACCAACAGATGTGGAGAAGTGGTTCCATCACCAGAAAAGC

Alignment

ORF - retro_cfam_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SEERAAP-TLEYRAFLKNEKGQYISPFHDVPIYADKDVFHMVVEVPRWSNAKMEI-ATKDPLNPIKQDVK
          S.E.AAP.TLEYR.FLKNEK.QYISPFHDV.IYADK..FHMVVE.P.WSNAK.EI.ATKDPLNPIKQDVK
Retrocopy SKEHAAPFTLEYRVFLKNEKEQYISPFHDVLIYADKHIFHMVVEAPHWSNAKKEI>ATKDPLNPIKQDVK

Parental  K-GKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVKVLGI
          K.GKLRYVANLFPY.GYI.NYGAIPQTWEDPGHNDK.TGCCGDNDPIDVCEIGSKVCARGEI.RVKVLGI
Retrocopy K<GKLRYVANLFPYTGYICNYGAIPQTWEDPGHNDKRTGCCGDNDPIDVCEIGSKVCARGEILRVKVLGI

Parental  LAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENQFAFNAEFKDK
          LAM.DEGET.WK.IAINVDDPDAANYNDI.DVK.LKPGYLEATVDWFRRYK.P.GKPE.QFA.NAEFKDK
Retrocopy LAMTDEGETGWKIIAINVDDPDAANYNDIYDVKWLKPGYLEATVDWFRRYKIPGGKPESQFALNAEFKDK

Parental  DFAMDIIKSTHDHWRALVTKKI-DGKGISCMNTTVSESPFKCDPDAAKAIVDALPPPCESACTVPTDVDK
          DFA.DIIKSTH..WRA.V.KKI..GKGISCMNT.VSE.PFKCD.DAA.AIVDALPPPC.SACTVPTDV.K
Retrocopy DFATDIIKSTHNRWRASVMKKI<RGKGISCMNTMVSERPFKCDSDAAEAIVDALPPPCQSACTVPTDVEK

Parental  WFHHQKN
          WFHHQK.
Retrocopy WFHHQKS

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	29.86 RPM
SRP017611_brain	0.00 RPM	72.49 RPM
SRP017611_kidney	0.13 RPM	55.80 RPM
SRP017611_liver	0.07 RPM	48.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1040 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405,
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040 ,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,