RetrogeneDB ID: retro_nleu_2242

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397338.1:6241702..6242281(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000011139
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSNLEG00000010034
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_nleu_2242
GAGAAAGATGAAGCTCTAGAAGATGAAGACAAGAAAAAAGATGATGGCATCTCATTCAGTAATCAGACAGGCCCTGCTTG
GGTAGGCTCAGAAAGAGACTACACATACGAGCAGCTGCTGAATCGAGTGTTCAACATCATGAGGGAAAAGAATCCAGATA
TGGTTGCTGGGGAGAAAAGGAAATTTGTCACGAAACCTCCACAGATCGTCCGAGTAGGAACCAAGAAAACTTCTTTTGTC
AACTTTACAGATATCTGTAAACTATTACATCATCAGCCCAAACATCTCCTTGCATTTTTGTTGGCTGAATTGGGTACAAG
TGGTTCTTTGGATGGTAATAACCAACTTGTAATCAAAGGAAGATTCCAATGGAAACAGATAGAAAATGTCTTGAGAAGAT
ATACCAAGGAATATGTCACTTGTCACACATACCGATCACCGGACACAATCCTGTAGAAGGACACGCGACTCTATTTCCTA
CAGTACGAAACTTGTCATTCTAGATGTTCTATTGCCAGTATCAAAACCGGCTTCCAGGCTGTCATGGGGAAGCGAGCACA
GTTCCGTGCCAAAGCTAAC

Alignment

ORF - retro_nleu_2242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.06 %
• Parental protein coverage: 59.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEDEILEKDEGNAEDSAAHLEVTQAFGPGLLDGGELYT-PALLNRVFNIMREKNPDMVAGEKRKFVMKPP
          ..DE.LE.......D.......T...GP........YT...LLNRVFNIMREKNPDMVAGEKRKFV.KPP
Retrocopy EKDEALEDEDKKKDDGISFSNQT---GPAWVGSERDYTYEQLLNRVFNIMREKNPDMVAGEKRKFVTKPP

Parental  QVVRVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKE
          Q.VRVGTKKTSFVNFTDICKLLH.QPKHLLAFLLAELGTSGS.DGNNQLVIKGRFQ.KQIENVLRRY.KE
Retrocopy QIVRVGTKKTSFVNFTDICKLLHHQPKHLLAFLLAELGTSGSLDGNNQLVIKGRFQWKQIENVLRRYTKE

Parental  YVTCHTCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          YVTCHT.RSPDTIL.KDTRLYFLQ.ETCHSRCS.ASIKTGFQAV.GKRAQ.RAKAN
Retrocopy YVTCHTYRSPDTIL*KDTRLYFLQYETCHSRCSIASIKTGFQAVMGKRAQFRAKAN

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2242 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Homo sapiens	ENSG00000125977	3 retrocopies	retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla	ENSGGOG00000015546	5 retrocopies	retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus	ENSMICG00000006944	1 retrocopy	retro_mmur_1583,
Macaca mulatta	ENSMMUG00000018095	1 retrocopy	retro_mmul_1483,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Nomascus leucogenys	ENSNLEG00000010034	2 retrocopies	retro_nleu_2242 , retro_nleu_466,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Pan troglodytes	ENSPTRG00000013412	2 retrocopies	retro_ptro_1600, retro_ptro_508,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,