RetrogeneDB ID: retro_ptro_2210

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:174005463..174006204(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSPTRG00000002585
• Aliases: None
• Description: None

Sequence

>retro_ptro_2210
ATGAGCGGCTTCAGCACTGAGGAGCACGCCACGCCCTTCTCCCTGGAGTACCGAGTCTTCCTCAAAAATGAGAAAGGACA
ATATATCTCTCCATTTCACGATATTCCAGTTTATGCAGATAAGGATGTGTTCCACAGGGTAGTTGAAGTTCCACGGTGGT
CTAATGCAAAAATGGAGGTTGCTACAAAGGACCCTTTAAACCCCATTAAACAAGATGTGAAAAAAAGAAAACTTCGCTAT
GTTGCAAATTTGTTCCCGTATAAAGGATATATCTGGAACTATGGTGCCATCCCTCAGACTTGGGAAGACCCAGGGCACAA
TGATAAACATACTGGCTGTTGTGGTGACAATGACCCAACTGATGTGTGTGAAATTGGAAGCAAGGTATGTGCAAGAGGTG
AAATAATTGGTGTGAAAGTTCTAGGCATATTGGCTATGACTGAGGAAGGGGAAACCGACTGGAAAGTCATTGCCATTAAT
ATGGATGATCCTGATGCAGCCAATTATAATGATATCAATGATGTCAAACGGCTGAAACCCAGCTACTTAGAGGCTACTGT
GGACTGGTTTAGAAGGTATAAGTTTCCTGATGGAAAACCAGAAAATGAGTTTGCTTTTAATGCAGAATTTAAAGATAAGG
ACTTTGCAATTGATATTATTAAAAGCACTCATGACCACTGGAAAGCATTAGTGACTAAGAAAACGAATGGAAAAGGAATC
AGTTGCATGAACACAACTGTG

Alignment

ORF - retro_ptro_2210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 85.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGFSTEERAAPFSLEYRVFLKNEKGQYISPFHDIPIYADKDVFHMVVEVPRWSNAKMEIATKDPLNPIK
          M.GFSTEE.A.PFSLEYRVFLKNEKGQYISPFHDIP.YADKDVFH.VVEVPRWSNAKME.ATKDPLNPIK
Retrocopy MSGFSTEEHATPFSLEYRVFLKNEKGQYISPFHDIPVYADKDVFHRVVEVPRWSNAKMEVATKDPLNPIK

Parental  QDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVKV
          QDVKK.KLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDP.DVCEIGSKVCARGEIIGVKV
Retrocopy QDVKKRKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPTDVCEIGSKVCARGEIIGVKV

Parental  LGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGKPENEFAFNAEF
          LGILAM..EGETDWKVIAIN.DDPDAANYNDINDVKRLKP.YLEATVDWFRRYK.PDGKPENEFAFNAEF
Retrocopy LGILAMTEEGETDWKVIAINMDDPDAANYNDINDVKRLKPSYLEATVDWFRRYKFPDGKPENEFAFNAEF

Parental  KDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTV
          KDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTV
Retrocopy KDKDFAIDIIKSTHDHWKALVTKKTNGKGISCMNTTV

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
SRP007412_brain_prefrontal_cortex	0.18 RPM	99.35 RPM
SRP007412_cerebellum	0.04 RPM	81.09 RPM
SRP007412_heart	0.03 RPM	48.41 RPM
SRP007412_kidney	0.08 RPM	69.01 RPM
SRP007412_liver	0.10 RPM	95.45 RPM
SRP007412_testis	0.11 RPM	65.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2210 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2210 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3267

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014023	1 retrocopy	retro_cpor_615,
Homo sapiens	ENSG00000180817	2 retrocopies	retro_hsap_2756, retro_hsap_3267,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Myotis lucifugus	ENSMLUG00000017790	1 retrocopy	retro_mluc_2469,
Macaca mulatta	ENSMMUG00000006397	1 retrocopy	retro_mmul_1540,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Oryctolagus cuniculus	ENSOCUG00000016001	2 retrocopies	retro_ocun_1373, retro_ocun_883,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pan troglodytes	ENSPTRG00000002585	2 retrocopies	retro_ptro_1864, retro_ptro_2210 ,
Tupaia belangeri	ENSTBEG00000008947	3 retrocopies	retro_tbel_3560, retro_tbel_3561, retro_tbel_848,
Tarsius syrichta	ENSTSYG00000005511	1 retrocopy	retro_tsyr_1856,