RetrogeneDB ID:

retro_pabe_2963

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:73634117..73634643(-)
Located in intron of:ENSPPYG00000016769
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBPMS2
Ensembl ID:ENSPPYG00000006553
Aliases:None
Description:RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]


Retrocopy-Parental alignment summary:






>retro_pabe_2963
ATCAGCGGCCTCCCCATGGACACTAAACCCAGAGAACCCTACTTGATCTTCCAGCCGTCCAAGGGGTATGAAGAGTCCCT
AATCAAGCTCACCGCGAGACAGCCTGTTTGTTTTGTGATCTTTGACAGCTGGACAGGAGCAGAAGCGGCCAAAAATGCGC
TGAACGATATTCGCTTAGATCCCGAAAACCCACAGATCATGAGGCTAGAGTTTGCCAAAGCCAACACCAAGATGGCCAAG
AGCAAGCTAATGGCAACTCCAAATCCCACCAACATGCACTCCACCTAGGAACACATTTACTTCATCGCTCGGGACCCCTA
TGACCTGATGGGGGCTGCTCTGATCCCTGCACCCCCAGAGGCCTGGGCCCTTAACCTTTGTACACCACAGAGCTGACCCC
AGCCATCACCCATGCTGCATTCACCTACCCAGCTGCCACTACCATTGCCGCCGCCCTCCATGCCAGGTGCGCTAGTTCCC
TTCCTCTGACACCACCCAGCAAGGATGGAAGTATCGTCAGTTCTGT

ORF - retro_pabe_2963 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.9 %
Parental protein coverage: 79.46 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTARQPVGFVIFDSRAGAEAGKNALNGIRFDPENPQTLRLE
.SGLP.D.KPRE.YL.F.P.KGYE.SLIKLTARQPV.FVIFDS..GAEA.KNALN.IR.DPENPQ..RLE
RetrocopyISGLPMDTKPREPYLIFQPSKGYEESLIKLTARQPVCFVIFDSWTGAEAAKNALNDIRLDPENPQIMRLE
ParentalFAKANTKIQLAKESKLMATPNPSNVHPA-LGAHFIARDPYDLMGAALIPASPEAWA-PYPLYTTELTPAI
FAKANTK......SKLMATPNP.N.H.......FIARDPYDLMGAALIPA.PEAWA.P.PLYTTELTPAI
RetrocopyFAKANTKM---AKSKLMATPNPTNMHST*EHIYFIARDPYDLMGAALIPAPPEAWA<P*PLYTTELTPAI
ParentalSHAAFTYPAATAAAAALHA-QVRWYPSSDTTQQGWKYRQFC
.HAAFTYPAAT..AAALHA.QVR..PSSDTTQQGWKYRQFC
RetrocopyTHAAFTYPAATTIAAALHA<QVR*FPSSDTTQQGWKYRQFC

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 .83 RPM 0 .94 RPM
SRP007412_cerebellum 0 .24 RPM 0 .00 RPM
SRP007412_heart 3 .25 RPM 6 .14 RPM
SRP007412_kidney 1 .46 RPM 3 .05 RPM
SRP007412_liver 0 .43 RPM 0 .92 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_2963 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2963 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2963 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3613
Pan troglodytes retro_ptro_2441
Gorilla gorilla retro_ggor_2438
Macaca mulatta retro_mmul_1837
Parental genes homology:
Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000110371 retrocopy
retro_btau_1674,
Callithrix jacchus ENSCJAG000000052002 retrocopies
retro_cjac_1775, retro_cjac_298,
Dipodomys ordii ENSDORG000000040251 retrocopy
retro_dord_438,
Homo sapiens ENSG000001668312 retrocopies
retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla ENSGGOG000000089841 retrocopy
retro_ggor_2438,
Loxodonta africana ENSLAFG000000187256 retrocopies
retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta ENSMMUG000000132701 retrocopy
retro_mmul_1837,
Monodelphis domestica ENSMODG000000104871 retrocopy
retro_mdom_571,
Mus musculus ENSMUSG000000323879 retrocopies
retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys ENSNLEG000000125051 retrocopy
retro_nleu_2209,
Otolemur garnettii ENSOGAG000000260171 retrocopy
retro_ogar_3254,
Pongo abelii ENSPPYG00000006553 1 retrocopy
retro_pabe_2963 ,
Pan troglodytes ENSPTRG000000071652 retrocopies
retro_ptro_1458, retro_ptro_2441,
Sus scrofa ENSSSCG000000045491 retrocopy
retro_sscr_851,
Ictidomys tridecemlineatus ENSSTOG000000100552 retrocopies
retro_itri_1512, retro_itri_556,
Tarsius syrichta ENSTSYG000000089963 retrocopies
retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus ENSTTRG000000118403 retrocopies
retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,


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