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


Retrocopy-Parental alignment summary:






>retro_pabe_1955
TCTGGAGACAAGATGATTTTTGATCCTACTATGAGCAGGAAGAAAAAGAAGTCATTTATGTTAGATGAGGGTGGGGATAC
CTAAACAGAGGAAAGCTAGCCCTCAGAAATAAAAGAAATGGAGCCAGAGCCAAATGAAGACAAAGATTTGGAAGCTGATG
AAGAGGACAATAGGAAAAGAGATGCTTTTGATGATCCGAATGACTTGATCTTCTTTAATCAAAAGAAAAAGAAGAGAAAA
ACAAAAAAGATATTTCAAATTGATGGAGGTGAAGAAGATGTAAAGGTTCTTAAGGCTGAAAGTGATATTTAAGAACCAGC
TGAACCAGGGGATGACATTGACATTATGTTTGTCAATAAAAAGAAGGAAAAGAGGAATTTCAGGTTCACAGATGAGAATA
AAATACTAGAGAAAGATGAAGCCTAAAAGATAAAAGACAGCAAAAAAAGACGATGTTATTTCATTCAGTAATCAGAGAGG
ATCTACTTGGGCAAGCTCAAAAAGAGACTACACATATGAGAAGCTACTGAATAGAGTGTTCCACATCATG

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:

ParentalSGDEMIFDPTMSKKKKKKKKPFMLDEEGDTQTEETQPSETKEVEPEPTEDKDLEADEEDTRKKDASDDLD
SGD.MIFDPTMS....KKKK.FMLDE.GDT.TEE..PSE.KE.EPEP.EDKDLEADEED.RK.DA.DD..
RetrocopySGDKMIFDPTMSR---KKKKSFMLDEGGDT*TEES*PSEIKEMEPEPNEDKDLEADEEDNRKRDAFDDPN
ParentalDLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDVQEPTEPEDDLDIMLGNKKKKKKNVKFPDEDEILE
DL.FFN...........F.ID..EE.VK.LK.ESD..EP.EP.DD.DIM..NKKK.K.N..F.DE..ILE
RetrocopyDLIFFNXXXXXXXXXXXFQIDGGEEDVKVLKAESDI*EPAEPGDDIDIMFVNKKKEKRNFRFTDENKILE
ParentalKDEALEDEDN-KKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIM
KDEA....D..KKDD.ISFSNQ.G..WA.S.RDYTYE.LLNRVF.IM
RetrocopyKDEA*KIKDS>KKDDVISFSNQRGSTWASSKRDYTYEKLLNRVFHIM

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1955 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1955 was not experimentally validated.

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

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000074981 retrocopy
retro_cfam_2070,
Choloepus hoffmanni ENSCHOG000000065211 retrocopy
retro_chof_271,
Callithrix jacchus ENSCJAG000000183342 retrocopies
retro_cjac_4196, retro_cjac_697,
Cavia porcellus ENSCPOG000000154391 retrocopy
retro_cpor_1143,
Echinops telfairi ENSETEG000000019221 retrocopy
retro_etel_1101,
Homo sapiens ENSG000001259773 retrocopies
retro_hsap_2176, retro_hsap_2260, retro_hsap_713,
Gorilla gorilla ENSGGOG000000155465 retrocopies
retro_ggor_1683, retro_ggor_1726, retro_ggor_2007, retro_ggor_280, retro_ggor_604,
Microcebus murinus ENSMICG000000069441 retrocopy
retro_mmur_1583,
Myotis lucifugus ENSMLUG000000053351 retrocopy
retro_mluc_604,
Macaca mulatta ENSMMUG000000180951 retrocopy
retro_mmul_1483,
Monodelphis domestica ENSMODG000000028055 retrocopies
retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus ENSMUSG000000746561 retrocopy
retro_mmus_3200,
Nomascus leucogenys ENSNLEG000000100342 retrocopies
retro_nleu_2242, retro_nleu_466,
Otolemur garnettii ENSOGAG000000014171 retrocopy
retro_ogar_196,
Pongo abelii ENSPPYG00000010933 2 retrocopies
retro_pabe_1955 , retro_pabe_2421,
Pan troglodytes ENSPTRG000000134122 retrocopies
retro_ptro_1600, retro_ptro_508,
Rattus norvegicus ENSRNOG000000174471 retrocopy
retro_rnor_2395,
Tupaia belangeri ENSTBEG000000099702 retrocopies
retro_tbel_1505, retro_tbel_2508,


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