RetrogeneDB ID: retro_ptro_508

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:92221705..92222441(-)
• 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_508
ATATTTGATATTGATGAAGCTGAAGAAGGTGTAAAGGATCTTAAGATTGAAAGTGATGTTCAAGAACCAACTGAACCAGA
GAATGACCTTGACATTATGCTTGGCAATAAAAAGAAGAAAAAGGTGGTCAAGTTCCCAGATGAGGATGAAATACTAGAGA
AAGATGAAGTTCTAGAAGAGGAAGACAGCAAAAAAGATGATGGTATCTCATTCAGTAATCAGACAGGCCCTGCTTGGGCA
GGCTCAGAAAGAGACTACACATATGAGGAGCTACTGAATCGAGTGTTCAACATCATGAGGGAAAAGAATCCAGGTATGGT
TGCTGGGGACATAAGGAAATTTGTCATGAAACCTCCACAGGTCGTCCGAGTAGGAACGAAGAAAACGTCTTTTGTCAACT
TTACACATATCTGTAAACTATTACATCATCAGCCCAAACATCTCCGTGCATTTTTGTTGGCTGAATTGGGTACAAGTGGT
TCTATAGATGGTAATAACCAACTTGTAATCAAAGGAAGATTCCAACAGAAACAGATAGAAAATGTCTTGAGAAGATATAT
CAAGGAATATGTCACTTGTCACACGTGCCGATTACTGGACACAATCCTGCAGAAGGACACGCAAATCTTATTTCCTACAG
TGTGAAACTTGTCATTCTAGATGTTCTGTTGCCAGCATCAAAACCAGCTACCAGGCTGTAATGGGCAAGTGAGCACACCA
CCGTGCCAAAGCTAAC

Alignment

ORF - retro_ptro_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.69 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIMLGNKKKKKKNVKFPDEDEILEKDEALEDEDNKKDDGI
          IFDIDEAEEGVKDLKIESDVQEPTEPE.DLDIMLGNKKKKK..VKFPDEDEILEKDE.LE.ED.KKDDGI
Retrocopy IFDIDEAEEGVKDLKIESDVQEPTEPENDLDIMLGNKKKKKV-VKFPDEDEILEKDEVLEEEDSKKDDGI

Parental  SFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVVRVGTKKTSFVNFTDICK
          SFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNP.MVAG..RKFVMKPPQVVRVGTKKTSFVNFT.ICK
Retrocopy SFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPGMVAGDIRKFVMKPPQVVRVGTKKTSFVNFTHICK

Parental  LLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRL
          LLH.QPKHL.AFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCR..DTILQKDT..
Retrocopy LLHHQPKHLRAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCHTCRLLDTILQKDTQI

Parental  -YFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          .YFLQCETCHSRCSVASIKT..QAV.GK.A..RAKAN
Retrocopy >YFLQCETCHSRCSVASIKTSYQAVMGK*AHHRAKAN

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	0.18 RPM	41.42 RPM
SRP007412_cerebellum	0.04 RPM	32.87 RPM
SRP007412_heart	0.17 RPM	44.77 RPM
SRP007412_kidney	0.03 RPM	45.53 RPM
SRP007412_liver	0.20 RPM	57.91 RPM
SRP007412_testis	0.42 RPM	74.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_508 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_508 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_713
Gorilla gorilla	retro_ggor_604

---

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,