RetrogeneDB ID: retro_ptro_1600

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:57936617..57937158(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSPTRG00000013412
• Aliases: None
• Description: Pan troglodytes eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa (EIF2S2), mRNA. [Source:RefSeq mRNA;Acc:NM_001098556]

Sequence

>retro_ptro_1600
ATGATTTTTGATCCTACTATGAGCAGGAAGAAAAAGAAGAAGTCATTTATGTTAGATGAGGGTGGGAATACCTAAACAGA
GGAAAGCTAACCCTGAGAAATAAAAGAAATGGAGCCAGAGCCAACTGAAGACAAAGATTTGGAAGCTGATGAAGAGGACA
ATAGGAAAAGAGATGCTTATGATGATCCAGATGACTTGATCTTCTTTAATCAAAAGAAAAAGAAGAGAAAAACAAAAAAG
ATATTTCATATTGATGGAGGTGAAGAAGATGTAAAGGTTCTTAAGATTGAAAGTGATATTTAAGAACCAGCTGAACCAGG
GGATGACCTTGACATTATGTTTGTCAATAAAAAGAAGGAAAGGAGGAATTTCAGGTTCACAGATGAGAATAAAATACTAG
AGAAAGATGAAGCCTAAAAGATAAAAGACAGCAAAAAAAGACCATGTTATCTCATTCAGTAATCAGACAGGCTCTATTTG
GGCAAACTCAAAAAGAGACTACACATATGAGAAGCTACTGAATAGAGTGTTCCACATCATG

Alignment

ORF - retro_ptro_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 55.49 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLDDLNF
          MIFDPTMS.KKKKK...FMLDE.G.T.TEE..P.E.KE.EPEPTEDKDLEADEED.RK.DA.DD.DDL.F
Retrocopy MIFDPTMSRKKKKKS--FMLDEGGNT*TEES*P*EIKEMEPEPTEDKDLEADEEDNRKRDAYDDPDDLIF

Parental  FNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIMLGNKKKKKKNVKFPDEDEILEKDEA
          FN...........F.ID..EE.VK.LKIESD..EP.EP.DDLDIM..NKKK...N..F.DE..ILEKDEA
Retrocopy FNXXXXXXXXXXXFHIDGGEEDVKVLKIESDI*EPAEPGDDLDIMFVNKKKERRNFRFTDENKILEKDEA

Parental  LEDEDN-KKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIM
          ....D..KKD..ISFSNQTG..WA.S.RDYTYE.LLNRVF.IM
Retrocopy *KIKDS>KKDHVISFSNQTGSIWANSKRDYTYEKLLNRVFHIM

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	41.42 RPM
SRP007412_cerebellum	0.00 RPM	32.87 RPM
SRP007412_heart	0.00 RPM	44.77 RPM
SRP007412_kidney	0.00 RPM	45.53 RPM
SRP007412_liver	0.00 RPM	57.91 RPM
SRP007412_testis	0.00 RPM	74.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1600 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1600 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2260
Pongo abelii	retro_pabe_1955

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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,