RetrogeneDB ID: retro_ptro_2566

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:130603599..130604703(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042432
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSPTRG00000010294
• Aliases: None
• Description: Mitogen-activated protein kinase kinase 2 [Source:UniProtKB/TrEMBL;Acc:K7BYT0]

Sequence

>retro_ptro_2566
GCAAACCTGGTGGACCTGCAGAAGAAGCTGGAGGAGCTGGAACTTGACGAGCAGCAGAAGTGGCCGGAAGCCTTTCTCAC
CCAGAAAGCCAAGGTCGGCGAACTCAAAGACGATGACTTCGAAAGGATCTCAGAGCTGGACGCGGGCAACGGCGGGGTGG
TCACCAAAGTCCAGCACAGACCCTCGGGCCTCATCATGGCCAGGAAGCTGATCCACCTTGAGATCAAGCCGGCCATCCGG
AACCAGATCATCCGCGAGCAACAGGTCCTGCACGAGTGCAACTCGCCGTACATCGTGGGCTTCTACGGGGCCTTCTACTG
TGACAGGGAGATCAGCATCTGCATGGAGCACATGGATGGCGGCTCCCTGGACCAGGGGCTGAAAGAGGCCAAGAGGATTC
CCGAGGACATCCTGGGGAAAGTCAGCATTGCGGTTCTCCGGGGCTTGGCGTACCTCCAAGAGAAGCACCAGATCATGCAC
CGAAATGTGAAGCCCTCCAACATCCTCGTGAACTCTAGAGGGGAGATCAAGCTGTGTGACTTCGGGGTGAGCGGCCAGCT
CATCGACTCCATGGCCAACTCCTTCGTGGGCACGCGCTCCTACATGGCTCCGGAGCGGTTGCAGGGCACACATTACTCGG
TGCAGTCGGTCTTCTGGAGCATGGACCTGTCCCTGGTGGAGCTGGTCATCGAAAGGTACCCCATCCCCCCGCCCGACGCC
AAGGAGCTGGAGGCCATCTTTGGCCGGCCCGTGGTCGACAGGGAAGAAGGAGAGCCTCACAGCATCTCCTCTTGGCCAGG
GTCCCCCGGGCGCCCCAACAGCGGTCACGGGATGGACAGCCGGCCCGCCATGGCCATCTTCGAACTGCTGGACTATATTG
TGAAAGAGCCGCCTCCTAAGCTGCCCAACGGTGTGTTCACCCCCGACTTCCAGGAGTTTGTCAATAAATGCCTCATCAAA
AACCCAACGGAGCGGGCGGACCTAAAGATGCTCACAAACCACGCCTTCATCAAGCGGTCCGAGGTGAAAGAAGCGGATTT
TGCCTGCTAGTTGTGTAAAACCCTGGGGCTGAACCAGCCCGGCACACCCACGCGCACCGCCGTG

Alignment

ORF - retro_ptro_2566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANLVDLQKKLEELELDEQQKKRLEAFLTQKAKVGELKDDDFERISELGAGNGGVVTKVQHRPSGLIMARK
          ANLVDLQKKLEELELDEQQK...EAFLTQKAKVGELKDDDFERISEL.AGNGGVVTKVQHRPSGLIMARK
Retrocopy ANLVDLQKKLEELELDEQQKWP-EAFLTQKAKVGELKDDDFERISELDAGNGGVVTKVQHRPSGLIMARK

Parental  LIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKEAKRIPEEILG
          LIHLEIKPAIRNQIIRE.QVLHECNSPYIVGFYGAFY.D.EISICMEHMDGGSLDQ.LKEAKRIPE.ILG
Retrocopy LIHLEIKPAIRNQIIREQQVLHECNSPYIVGFYGAFYCDREISICMEHMDGGSLDQGLKEAKRIPEDILG

Parental  KVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMAPERLQG
          KVSIAVLRGLAYL.EKHQIMHR.VKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMAPERLQG
Retrocopy KVSIAVLRGLAYLQEKHQIMHRNVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMAPERLQG

Parental  THYSVQSDIWSMGLSLVELAVGRYPIPPPDAKELEAIFGRPVVDGEEGEPHSISPRPRPPGRPVSGHGMD
          THYSVQS..WSM.LSLVEL...RYPIPPPDAKELEAIFGRPVVD.EEGEPHSIS..P..PGRP.SGHGMD
Retrocopy THYSVQSVFWSMDLSLVELVIERYPIPPPDAKELEAIFGRPVVDREEGEPHSISSWPGSPGRPNSGHGMD

Parental  SRPAMAIFELLDYIVNEPPPKLPNGVFTPDFQEFVNKCLIKNPAERADLKMLTNHTFIKRSEVEEVDFAG
          SRPAMAIFELLDYIV.EPPPKLPNGVFTPDFQEFVNKCLIKNP.ERADLKMLTNH.FIKRSEV.E.DFA.
Retrocopy SRPAMAIFELLDYIVKEPPPKLPNGVFTPDFQEFVNKCLIKNPTERADLKMLTNHAFIKRSEVKEADFAC

Parental  WLCKTLRLNQPGTPTRTAV
          .LCKTL.LNQPGTPTRTAV
Retrocopy *LCKTLGLNQPGTPTRTAV

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	2.50 RPM	97.02 RPM
SRP007412_cerebellum	1.08 RPM	44.99 RPM
SRP007412_heart	0.35 RPM	19.94 RPM
SRP007412_kidney	1.12 RPM	60.20 RPM
SRP007412_liver	1.21 RPM	60.85 RPM
SRP007412_testis	3.90 RPM	25.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2566 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2566 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3785
Gorilla gorilla	retro_ggor_115

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015084	1 retrocopy	retro_cjac_4061,
Equus caballus	ENSECAG00000009157	2 retrocopies	retro_ecab_668, retro_ecab_968,
Homo sapiens	ENSG00000126934	1 retrocopy	retro_hsap_3785,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
Nomascus leucogenys	ENSNLEG00000003013	1 retrocopy	retro_nleu_1121,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566 ,