RetrogeneDB ID: retro_pabe_1955

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:53939511..53940061(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSPPYG00000010933
• Aliases: None
• Description: eukaryotic translation initiation factor 2 subunit 2 [Source:RefSeq peptide;Acc:NP_001127646]

Sequence

>retro_pabe_1955
TCTGGAGACAAGATGATTTTTGATCCTACTATGAGCAGGAAGAAAAAGAAGTCATTTATGTTAGATGAGGGTGGGGATAC
CTAAACAGAGGAAAGCTAGCCCTCAGAAATAAAAGAAATGGAGCCAGAGCCAAATGAAGACAAAGATTTGGAAGCTGATG
AAGAGGACAATAGGAAAAGAGATGCTTTTGATGATCCGAATGACTTGATCTTCTTTAATCAAAAGAAAAAGAAGAGAAAA
ACAAAAAAGATATTTCAAATTGATGGAGGTGAAGAAGATGTAAAGGTTCTTAAGGCTGAAAGTGATATTTAAGAACCAGC
TGAACCAGGGGATGACATTGACATTATGTTTGTCAATAAAAAGAAGGAAAAGAGGAATTTCAGGTTCACAGATGAGAATA
AAATACTAGAGAAAGATGAAGCCTAAAAGATAAAAGACAGCAAAAAAAGACGATGTTATTTCATTCAGTAATCAGAGAGG
ATCTACTTGGGCAAGCTCAAAAAGAGACTACACATATGAGAAGCTACTGAATAGAGTGTTCCACATCATG

Alignment

ORF - retro_pabe_1955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 55.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGDEMIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLD
          SGD.MIFDPTMS....KKKK.FMLDE.GDT.TEE..PSE.KE.EPEP.EDKDLEADEED.RK.DA.DD..
Retrocopy SGDKMIFDPTMSR---KKKKSFMLDEGGDT*TEES*PSEIKEMEPEPNEDKDLEADEEDNRKRDAFDDPN

Parental  DLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIMLGNKKKKKKNVKFPDEDEILE
          DL.FFN...........F.ID..EE.VK.LK.ESD..EP.EP.DD.DIM..NKKK.K.N..F.DE..ILE
Retrocopy DLIFFNXXXXXXXXXXXFQIDGGEEDVKVLKAESDI*EPAEPGDDIDIMFVNKKKEKRNFRFTDENKILE

Parental  KDEALEDEDN-KKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIM
          KDEA....D..KKDD.ISFSNQ.G..WA.S.RDYTYE.LLNRVF.IM
Retrocopy KDEA*KIKDS>KKDDVISFSNQRGSTWASSKRDYTYEKLLNRVFHIM

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	0.00 RPM	37.98 RPM
SRP007412_cerebellum	0.00 RPM	51.80 RPM
SRP007412_heart	0.00 RPM	35.25 RPM
SRP007412_kidney	0.00 RPM	39.01 RPM
SRP007412_liver	0.00 RPM	44.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1955 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1955 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2260
Pan troglodytes	retro_ptro_1600

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
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,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
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,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
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,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,