RetrogeneDB ID:

retro_ptro_3200

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:41281399..41282305(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SDCBP
Ensembl ID:ENSPTRG00000020277
Aliases:SDCBP, syntenin-1
Description:Pan troglodytes syndecan binding protein (syntenin) (SDCBP), mRNA. [Source:RefSeq mRNA;Acc:NM_001246446]


Retrocopy-Parental alignment summary:






>retro_ptro_3200
AAGAACCCTGCAAAAATGTCTCTCTATCCATCTCTTGAAAACTTGAAGGTAGACAAAGTAATTGGGGCTCAAACTACTTT
TTCTACAAACTCTGCCAATCCAGCAATTTTGTCAGAAGCTTCTGCTCCCATCTCTCAAAATGGAAATCTCTATCCCAAAT
TATATCCAGAGCTCTCTCAATACATGGGCCTGAGTTTAAATGAAGAAGAAATATGTGCAAATGTGGCCATGGTTTCTGGT
GCACCAATTCAGGGGCAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTGGCTGCTGTAACTGGTAATGATGTTGG
AATTCACAGAGCAGAAATTAAGCAAGGGATTTGTGAAGTCATTTTGTGTAAGGATCACAATGGAAAAATTGGACTCAGGC
TTAAATCAATAGATAATGGTATATTTGTTCAGCTAGTCCAGGCTAATTCTCCAGCCTCATTGGTTGGTCTGAGAATTGAG
GACCAAGTACTCCAGATTAATAGTGAAAACTGTGCAGGGTAGAGCTCTGATAAAGCACACAAGGTGCTCAAACAGAATTT
TGGAGAGATTACCATGACCATTCATGACAGGCCGTTTGAATGGACGATTACCATGCATAAGGATAGCACTGGACATGTTG
GTTTTATCTTTAAAAATGGACAAATAACATCCATAGTGAAAGATAGCTCTGCAGCCAGAAATGGTCTTCTCACAGAACAT
AACATCTGTGAAATCAATGGACAGAATGTCATTGAATCGAAGGACTCTCAAACTGCAGACATACTGTCAACATCTGGGAC
TGTAGTTACTATTACAATCATGCCTGCTTTTATCTTTGAACATATTATTAAGCGGATGGCACCAAGCATTATGAAAAGCC
TAATGGACCACACCATTTCTGAGGTT

ORF - retro_ptro_3200 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.44 %
Parental protein coverage: 94.97 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKNPAKMSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEE
KNPAKMSLYPSLE.LKVDKVI.AQT.FS.N.ANPAILSEASAPI...GNLYP.LYPELSQYMGLSLNEEE
RetrocopyKNPAKMSLYPSLENLKVDKVIGAQTTFSTNSANPAILSEASAPISQNGNLYPKLYPELSQYMGLSLNEEE
ParentalIRANVAVVSGAPLQG-LVARPSSINYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNG
I.ANVA.VSGAP.QG.LVARPSS.NYMVA.VTGNDVGI.RAEIKQGI.EVILCKD..GKIGLRLKSIDNG
RetrocopyICANVAMVSGAPIQGQLVARPSSMNYMVAAVTGNDVGIHRAEIKQGICEVILCKDHNGKIGLRLKSIDNG
ParentalIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDS
IFVQLVQANSPASLVGLR..DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFE.TITMHKDS
RetrocopyIFVQLVQANSPASLVGLRIEDQVLQINSENCAG*SSDKAHKVLKQNFGE-ITMTIHDRPFEWTITMHKDS
ParentalTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIF
TGHVGFIFKNG.ITSIVKDSSAARNGLLTEHNICEINGQNVI..KDSQ.ADILSTSGTVVTITIMPAFIF
RetrocopyTGHVGFIFKNGQITSIVKDSSAARNGLLTEHNICEINGQNVIESKDSQTADILSTSGTVVTITIMPAFIF
ParentalEHIIKRMAPSIMKSLMDHTIPEV
EHIIKRMAPSIMKSLMDHTI.EV
RetrocopyEHIIKRMAPSIMKSLMDHTISEV

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 .04 RPM 56 .39 RPM
SRP007412_cerebellum 0 .00 RPM 35 .60 RPM
SRP007412_heart 0 .06 RPM 68 .96 RPM
SRP007412_kidney 0 .08 RPM 65 .75 RPM
SRP007412_liver 0 .13 RPM 52 .05 RPM
SRP007412_testis 0 .00 RPM 36 .67 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3200 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3200 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3200 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4810
Gorilla gorilla retro_ggor_2995
Pongo abelii retro_pabe_3738
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 ENSPPYG000000186123 retrocopies
Pan troglodytes ENSPTRG00000020277 2 retrocopies
retro_ptro_2696, retro_ptro_3200 ,
Tupaia belangeri ENSTBEG000000139651 retrocopy



Copyright © RetrogeneDB 2014-2017