RetrogeneDB ID: retro_cfam_405

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:64682470..64683347(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000003191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPA2
• Ensembl ID: ENSCAFG00000010887
• Aliases: None
• Description: pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]

Sequence

>retro_cfam_405
CGCACAGGGCCTGGCCCACACTGCGCCATGGCTTCCTACTGCACAGAGGAGCACAGCCAGCCCCGCTCCCCCAGTTACCA
CCTCTTCTTCAAGAATGTAGCTGGTCACTACATTTCCCCCTTTCATGATATTCCTCTGAAGGTGGACTCAACAGTGGAAA
ATGGCATTCCTACAAAGAGAGCACGAAATGATGAGTATGAGAATTTGTTTAATATGGTTGTAGAAGTACCTCGGTGGACA
AATGCTAAAATGGAGATTGCCACAAAAGAGCCTTTGAATCCCATTAAACAAGATAGAAAGGATGGCAAGCTACAGTACGT
GGCGAATATCTTCCCTCACAAGGGTTATATTTGGAATTACGGTGCCCTCCCACAGACTTGGGAAGATCCCCATCGAAAAG
ATAAGAGTACAGACTGCTGTGGAGATAATGATCCTATGTGATGTTTGCGAAATAGGCTCAAAGGTTCTTTCTTGTGGAGA
GGTTATTCCTGTGAAGATCCTTGGAATTTTGGCTCTTATTGATCAGGGTGAAACAGATTGGAAAATAATTGCTATCAATG
TGAATGATCCTGAAGCCTCAAAGTTTCATGATATTGATGATGTTAAGAAGTACAAACCAGGTTACTTGGAAGCTACGCTT
AACTGGTTTAGATTTTATAAGGTGCCAGAAGGAAAACCAGAAAACCAGTTTGCTTTTAATGCAGAATTCAAAAACAAGGC
TTTTGCTCTTGATGTTATTAAATCTACTCATGAATGCTGGAAAGCATTGCTTATGAAGAAGTGTGATGGAGGAGCTATAA
AGTGCACAAATGTGCATATATCTGACAGCCCTTTCCATTGCACTCAAGAGGAAGCAAGATCAATAGTTGAACTGGTG

Alignment

ORF - retro_cfam_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.2 %
• Parental protein coverage: 85.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAGPGPHRAMASYRTEERGRPRSPGYRLFFQNVAGHYISPFHDIPLKVDSTEENGIPTKRARSDEYENLF
          R.GPGPH.AMASY.TEE...PRSP.Y.LFF.NVAGHYISPFHDIPLKVDST.ENGIPTKRAR.DEYENLF
Retrocopy RTGPGPHCAMASYCTEEHSQPRSPSYHLFFKNVAGHYISPFHDIPLKVDSTVENGIPTKRARNDEYENLF

Parental  NMVVEVPRWTNAKMEIATKEPLNPIKQDIKDGKLRYVANIFPHKGYIWNYGALPQTWEDPHRKDKSTDCC
          NMVVEVPRWTNAKMEIATKEPLNPIKQD.KDGKL.YVANIFPHKGYIWNYGALPQTWEDPHRKDKSTDCC
Retrocopy NMVVEVPRWTNAKMEIATKEPLNPIKQDRKDGKLQYVANIFPHKGYIWNYGALPQTWEDPHRKDKSTDCC

Parental  GDNDPI-DVCEIGSKVLSCGEVIPVKILGILALIDQGETDWKIIAINVNDPEASKFHDIDDVKKYKPGYL
          GDNDP..DVCEIGSKVLSCGEVIPVKILGILALIDQGETDWKIIAINVNDPEASKFHDIDDVKKYKPGYL
Retrocopy GDNDPM>DVCEIGSKVLSCGEVIPVKILGILALIDQGETDWKIIAINVNDPEASKFHDIDDVKKYKPGYL

Parental  EATLNWFRFYKVPEGKPENQFAFNGEFKNKAFALDVIKSTHECWKALLMKKCDGGAIKCTNVHICDSPFH
          EATLNWFRFYKVPEGKPENQFAFN.EFKNKAFALDVIKSTHECWKALLMKKCDGGAIKCTNVHI.DSPFH
Retrocopy EATLNWFRFYKVPEGKPENQFAFNAEFKNKAFALDVIKSTHECWKALLMKKCDGGAIKCTNVHISDSPFH

Parental  CTQEEARSIVELV
          CTQEEARSIVELV
Retrocopy CTQEEARSIVELV

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	0.13 RPM	7.14 RPM
SRP017611_brain	0.87 RPM	10.80 RPM
SRP017611_kidney	6.54 RPM	68.61 RPM
SRP017611_liver	0.58 RPM	5.87 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_405 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010887	1 retrocopy	retro_cfam_405 ,
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Choloepus hoffmanni	ENSCHOG00000008731	3 retrocopies	retro_chof_1052, retro_chof_430, retro_chof_769,
Echinops telfairi	ENSETEG00000014816	1 retrocopy	retro_etel_1959,
Macaca mulatta	ENSMMUG00000017004	1 retrocopy	retro_mmul_1278,
Monodelphis domestica	ENSMODG00000020635	5 retrocopies	retro_mdom_638, retro_mdom_795, retro_mdom_945, retro_mdom_946, retro_mdom_947,
Oryctolagus cuniculus	ENSOCUG00000005941	2 retrocopies	retro_ocun_1338, retro_ocun_1470,
Ochotona princeps	ENSOPRG00000007086	1 retrocopy	retro_opri_847,
Sus scrofa	ENSSSCG00000022365	1 retrocopy	retro_sscr_557,
Tursiops truncatus	ENSTTRG00000003141	2 retrocopies	retro_ttru_1307, retro_ttru_606,