RetrogeneDB ID:

retro_chof_970

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_177291:943..1627(+)
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:ENSCHOG00000003565
Aliases:None
Description:syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662]


Retrocopy-Parental alignment summary:






>retro_chof_970
AATATGGCTGTGGTTCCTGGAGAACCAGCACCAGGGTTAGTGGTAGGATCTTCCAGTGTGAACTATATGGTGGCTTCCAT
AACTGGTAATGTTGGAATTCAAAGAACAGAAATTAAGCAAAGGATTCATGAAGTTATTTTGTGTAAGGATCAAGACGGAA
AAATTGGCCTCTGGCTTAAATCAGTAGATGATGGTTTATTTATCCAGCTAGTCCAAGCTAATTCTCCAGCATTGTTGGTT
GGTCTGAGATTTGGGGATCAGGTACTCCAGATTAATGGTAAAAACTGTGCAGGCTGGAGCTCTGATAAAGCACACAAAGT
GCTCAAACTGGCTTTGAGAGAAAAAATTACTATGACTATTCATGACAGGCCCTTTGAATGGACTGTTACCATGCATACAG
ATAGTACTGGACATGTTGGCTTTATCTTTAAAAATGGAAAAATAATGTCCATAGTGAAAGATAGCTCTGCAAACAAAAAC
TGTCTTCCTACAGAATATAGTATCTGTGAAATCAATGGACAGAATGTCATTGGATTGAAGGACTCTCAAATTGCAGACAT
ACTTTCAACATCTGGAGCTGTAGTTACTGTTACAATCATGCCTGCTTTTATCTTTGAACATATTATTAAATGGATGTCAC
CAAGCATTATGAAAAGCCTGATGGATCACATCATTCCTGAGGTT

ORF - retro_chof_970 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.17 %
Parental protein coverage: 90.55 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNMVMVFGEPVQGQLVVRPSSVNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSVDNGVFI
NM..V.GEP..G.LVV..SSVNYMVA..TGN.VGI.R.EIKQ.I.EVILCKDQDGKIGL.LKSVD.G.FI
RetrocopyNMAVVPGEPAPG-LVVGSSSVNYMVASITGN-VGIQRTEIKQRIHEVILCKDQDGKIGLWLKSVDDGLFI
ParentalQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSSGH
QLVQANSPA.LVGLRFGDQVLQING.NCAGWSSDKAHKVLK.A..EKITMTI.DRPFE.T.TMH.DS.GH
RetrocopyQLVQANSPALLVGLRFGDQVLQINGKNCAGWSSDKAHKVLKLALREKITMTIHDRPFEWTVTMHTDSTGH
ParentalVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQTADILSTSGTVVTITIMPAFIFEHI
VGFIFKNGKI.SIVKDSSA..N.L.TE..ICEINGQNVIGLKDSQ.ADILSTSG.VVT.TIMPAFIFEHI
RetrocopyVGFIFKNGKIMSIVKDSSANKNCLPTEYSICEINGQNVIGLKDSQIADILSTSGAVVTVTIMPAFIFEHI
ParentalIKRMAPSIMKSLMDHTIPEV
IK.M.PSIMKSLMDH.IPEV
RetrocopyIKWMSPSIMKSLMDHIIPEV

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_970 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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 ENSCHOG00000003565 5 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 ENSPTRG000000202772 retrocopies
Tupaia belangeri ENSTBEG000000139651 retrocopy



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