RetrogeneDB ID:

retro_pabe_3738

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:41461552..41462443(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP459C0145
Ensembl ID:ENSPPYG00000018612
Aliases:None
Description:syntenin-1 [Source:RefSeq peptide;Acc:NP_001125892]


Retrocopy-Parental alignment summary:






>retro_pabe_3738
ATGTCTCTCTATCTATCTCTTGAAGACTTGAAGGTAGACAAAGTAATTGGGGCTCAAACTACTTTTTCTGCAAACTCTGC
CAATCCAGCAATTTTGTCAGAAGCTTCTGCTCCCATCTCTCAAAATGGAAATCTGTATCCCAAATTATATCCGGAGCTCT
CTCAATACATGGGCCTGAGTTTAAATGAAGAAGAAATATGTGCAAATGTGGCCATGGTTTCTGGTGCACCAATTCAAGGG
CAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTGGCTCCTGTAACTTGTAATGATGTTGGAATTCACAGAACAGA
AATTAAGCAAGGGATTCGTGAAGTCATTTTGTGTAACGATCAAGATGGAAAAATTGGACTCAGGCTTAAATCAATAGATA
ATGGTATATTTGTTCAGCTAGTCCAGGCTAATTCTCCAGCCTCATTGGTTGGTCTGACAATTGAGGACCAAGTACTCCAG
ATTAATAGTGAAAACTGTGCAGGGTAGAGCTCTGATAAAGCGCACAAGGTGCTCAAACAGGATTTTGGAGAGATTACCAT
GACCATTCATGACAGGCCCTTTGAACGGACGATTACCATGCATAAGGATAGCACTGGACATGTTGGTTTTATCTTTAAAA
ACGGAAAAATAACATCCATAGTGAAAGATAGCTCTGCAGCCAGAAGTGGTCTTCTCACAGAACATAACATCTGTGAAATC
AATGGACACAATGTCATTGAATTGAAGGACTCTCAAATTGCAGACATACTGTCAACATCTGGGACTGTAGTTACTATTAC
AATTATGCCTGCTTTTATCTTTGAACATATTATTAAGCGGATGGTACCAAGCATTATGAAAAGCCTAACGGACCACACCA
TTTCTGAGGTT

ORF - retro_pabe_3738 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.26 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEEIRANM
MSLY.SLEDLKVDKVI.AQT.FSAN.ANPAILSEASAPI...GNLYP.LYPELSQYMGLSLNEEEI.AN.
RetrocopyMSLYLSLEDLKVDKVIGAQTTFSANSANPAILSEASAPISQNGNLYPKLYPELSQYMGLSLNEEEICANV
ParentalAVVSGAPLQG-LVARPSSMNYMVAPVTGNDAGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQL
A.VSGAP.QG.LVARPSSMNYMVAPVT.ND.GI.R.EIKQGIREVILC.DQDGKIGLRLKSIDNGIFVQL
RetrocopyAMVSGAPIQGQLVARPSSMNYMVAPVTCNDVGIHRTEIKQGIREVILCNDQDGKIGLRLKSIDNGIFVQL
ParentalVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVG
VQANSPASLVGL...DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFERTITMHKDSTGHVG
RetrocopyVQANSPASLVGLTIEDQVLQINSENCAG*SSDKAHKVLKQDFGE-ITMTIHDRPFERTITMHKDSTGHVG
ParentalFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIFEHIIK
FIFKNGKITSIVKDSSAAR.GLLTEHNICEING.NVI.LKDSQIADILSTSGTVVTITIMPAFIFEHIIK
RetrocopyFIFKNGKITSIVKDSSAARSGLLTEHNICEINGHNVIELKDSQIADILSTSGTVVTITIMPAFIFEHIIK
ParentalRMAPSIMKSLMDHTIPEV
RM.PSIMKSL.DHTI.EV
RetrocopyRMVPSIMKSLTDHTISEV

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 1 .99 RPM 101 .24 RPM
SRP007412_cerebellum 0 .61 RPM 69 .80 RPM
SRP007412_heart 0 .60 RPM 52 .50 RPM
SRP007412_kidney 1 .92 RPM 151 .51 RPM
SRP007412_liver 1 .35 RPM 98 .97 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3738 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3738 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3738 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4810
Pan troglodytes retro_ptro_3200
Gorilla gorilla retro_ggor_2995
Macaca mulatta retro_mmul_2564

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

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000061611 retrocopy
Bos taurus ENSBTAG000000199102 retrocopies
Canis familiaris ENSCAFG000000071121 retrocopy
Choloepus hoffmanni ENSCHOG000000035655 retrocopies
Equus caballus ENSECAG000000150531 retrocopy
Homo sapiens ENSG000001375752 retrocopies
Gorilla gorilla ENSGGOG000000090192 retrocopies
Loxodonta africana ENSLAFG000000107571 retrocopy
Microcebus murinus ENSMICG000000039681 retrocopy
Myotis lucifugus ENSMLUG000000048071 retrocopy
Macaca mulatta ENSMMUG000000172961 retrocopy
Mustela putorius furoENSMPUG000000103395 retrocopies
Nomascus leucogenys ENSNLEG000000014082 retrocopies
Otolemur garnettii ENSOGAG000000134621 retrocopy
Procavia capensis ENSPCAG000000164321 retrocopy
Pongo abelii ENSPPYG00000018612 3 retrocopies
retro_pabe_3265, retro_pabe_3266, retro_pabe_3738 ,
Pan troglodytes ENSPTRG000000202772 retrocopies
Tupaia belangeri ENSTBEG000000139651 retrocopy



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