RetrogeneDB ID: retro_ogar_576

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873523.1:32443564..32444224(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033122
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSOGAG00000001658
• Aliases: None
• Description: mitogen-activated protein kinase kinase 2 [Source:HGNC Symbol;Acc:6842]

Sequence

>retro_ogar_576
ATCGTGGGCTTCTACCGGGCCTTCTACAGTGCCGGGGAGATCAGCATCTGCATGGAGCACATAGATGGTGGCTCCCTGGA
CCAGGTGCGGAAAGAAGCCAAAAGGAGTCCTGAGGAGATCCTGGGGAAAGTCAGCATTGCAGTCCTCCGGGGCTTGGCGT
ACCTCCGAGAAAAGCACCAGATCATGCACAGAGATGTGAAACTTTCCAACATCCTCCTCAACTCCAGTAGGGAGATTAAG
CTGTGTGATTTCGGGGTGAGCGGGCAGCTCATCGACTGCATGGCCAACTCCTTTGTAGGAACTCGATCCTACGTGTCTCC
GGAGCGGTTGCAAGGCACACACTATTCAGTGCAGTCTGACATCTGGAGCATGGGCCTGTCGCTGGTGGAGCTGTCCATTG
GAAGTACCCCATCCCTCCCCCGCCCGACACCAAGGAGCTGGAGGCCCTATTTGGCAGGGCCGTGCCAATGGGCTGGAAGG
AGAGGCCCACAGCATCTCGCCTCATCCGAGACCTCCTGGGCGCCCTCTGAGTGCAGGTCCCGGGCTGGACAGTCGGCCAG
CTATGGCCATCTTCGAGCTAGTGGACTACATTGTGAAAATGAGCCTCCTCCCAAGCTGCCCAACAGCGTGTTCACCCCAG
ACTTCCAGGAGTTTGTAAAT

Alignment

ORF - retro_ogar_576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 54.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IVGFYGAFYSDGEISICMEHMDGGSLDQVLKEAKRIPEEILGKVSIAVLRGLAYLREKHQIMHRDVKPSN
          IVGFY.AFYS.GEISICMEH.DGGSLDQV.KEAKR.PEEILGKVSIAVLRGLAYLREKHQIMHRDVK.SN
Retrocopy IVGFYRAFYSAGEISICMEHIDGGSLDQVRKEAKRSPEEILGKVSIAVLRGLAYLREKHQIMHRDVKLSN

Parental  ILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVELSIG-RYPI-
          IL.NS..EIKLCDFGVSGQLID.MANSFVGTRSY.SPERLQGTHYSVQSDIWSMGLSLVELSIG..YPI.
Retrocopy ILLNSSREIKLCDFGVSGQLIDCMANSFVGTRSYVSPERLQGTHYSVQSDIWSMGLSLVELSIG<KYPIP

Parental  PPPDAKELEALFGRAV-ADGLEGEAHSISPRPRPPGRPIS-GPGLDSRPAMAIFELLDYIV-NEPPP-KL
          PPPD.KELEALFGRAV.A.GLEGEAHSISP.PRPPGRP.S.GPGLDSRPAMAIFEL.DYIV....PP.KL
Retrocopy PPPDTKELEALFGRAV<ANGLEGEAHSISPHPRPPGRPLSAGPGLDSRPAMAIFELVDYIV<ENEPPPKL

Parental  PNSVFTPDFQEFVN
          PNSVFTPDFQEFVN
Retrocopy PNSVFTPDFQEFVN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_576 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,