RetrogeneDB ID:

retro_pabe_391

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:57554362..57554704(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ITGB1BP1
Ensembl ID:ENSPPYG00000012667
Aliases:ITGB1BP1, DKFZP459I196
Description:Integrin beta-1-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R5S7]


Retrocopy-Parental alignment summary:






>retro_pabe_391
CACAGTAGTAGCAGTTCCCAAAGTGGTGAAATCAGTACTAAGAGCAAGTCTGTAGATTCCAGCCTTGGGGGCCTTTCATA
GCCCAGCCCTGTGGCCAGCCTCAATACAGATTCCACCAAGAGTGCAGAATAAAGCAACAATAATTCAAATACGTGTGCAG
AACTTCAAATAAAATATGTTGGTGCCATTAAGACACTGAAACTCTCTGAGAGAAGATGTCTTGAAGGGCCACTAGACCTG
ATAAATTATATAGATGTTGCCCAGCAAGATGAAAAGTTGCCTCTTGTTCCTCTGGAGGAAAAATTTATAATGGGAGTTTC
CAAATATAATACAAGTATCAAC

ORF - retro_pabe_391 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.19 %
Parental protein coverage: 57. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNSNSDTCAEFRIKYVGAIEKLKLSE
HSSSSSQS.EISTKSKSVDSSLGGLS..S.VASL.TDSTKS...SN.NS.TCAE..IKYVGAI..LKLSE
RetrocopyHSSSSSQSGEISTKSKSVDSSLGGLS*PSPVASLNTDSTKSAE*SNNNSNTCAELQIKYVGAIKTLKLSE
ParentalGKDLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVS
...LEGPLDLINYIDVAQQD.KLP.VP.EE.FIMGVSKY.....
RetrocopyRRCLEGPLDLINYIDVAQQDEKLPLVPLEEKFIMGVSKYNTSIN

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






(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 54 .35 RPM
SRP007412_cerebellum 0 .00 RPM 49 .25 RPM
SRP007412_heart 0 .03 RPM 34 .83 RPM
SRP007412_kidney 0 .00 RPM 23 .27 RPM
SRP007412_liver 0 .00 RPM 12 .15 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_391 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_391 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_391 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_277
Pan troglodytes retro_ptro_231
Gorilla gorilla retro_ggor_321
Macaca mulatta retro_mmul_563

Parental genes homology:
Parental genes homology involve 19 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000130632 retrocopies
Choloepus hoffmanni ENSCHOG000000136022 retrocopies
Callithrix jacchus ENSCJAG000000062503 retrocopies
Dasypus novemcinctus ENSDNOG000000089303 retrocopies
Homo sapiens ENSG000001191851 retrocopy
Gorilla gorilla ENSGGOG000000017541 retrocopy
Macropus eugenii ENSMEUG000000067611 retrocopy
Microcebus murinus ENSMICG000000023597 retrocopies
Myotis lucifugus ENSMLUG000000106292 retrocopies
Macaca mulatta ENSMMUG000000180361 retrocopy
Nomascus leucogenys ENSNLEG000000133221 retrocopy
Oryctolagus cuniculus ENSOCUG000000037261 retrocopy
Otolemur garnettii ENSOGAG000000016794 retrocopies
Procavia capensis ENSPCAG000000059761 retrocopy
Pongo abelii ENSPPYG00000012667 1 retrocopy
retro_pabe_391 ,
Pan troglodytes ENSPTRG000000116371 retrocopy
Sorex araneus ENSSARG000000097991 retrocopy
Tarsius syrichta ENSTSYG000000145371 retrocopy
Tursiops truncatus ENSTTRG000000008591 retrocopy



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