RetrogeneDB ID:

retro_chof_258

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_5659:32520..32990(-)
Located in intron of:ENSCHOG00000008893
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EPCAM
Ensembl ID:ENSCHOG00000013834
Aliases:None
Description:epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]


Retrocopy-Parental alignment summary:






>retro_chof_258
CAAGAGAAAAACCTTATGATTTTGAGTCTGCGGACTGTTCTCGAGGAGGCAATCACAACTCGTTATAAACTGGATCCAAA
ATATATCATAAACATTCTGTGTGAGAATGATGTTATCACTATTGATCTGGTGGAAAATTCTTTCAGAAAACTCAGAATGA
TGTGGATATAGCTGACGTGGCTTATTATTTTGAAAAAGATGTTAAAGGTGAATCCTTATTCCATTCCAGTAGCATGGACC
TGAGAGTAAATGGGGAACAACTAGATCTCGATCCTGGTCAAAGTTTAATTTACTACGTTGATGAATTTTCAATGCAGGGT
CTAAAAGCTGGTATTATTGCTGTCATTGTGGTTGCAACAATAGCAGTTATTGCTGGAATTGTGCTGGTTATTTCCAGAAA
GAAGAGAATGACAAAGTATGAGAAGACTGAGATAAAGGAGATGGATGAGATGCATAGGAAACTCAATGCG

ORF - retro_chof_258 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.66 %
Parental protein coverage: 51.1 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalREKPYDFESLRTALEEAITTRYQLDPKYITNILYENDVITIDLVQNSS-QKTQNDVDIADVAYYFEKDVK
.EK.....SLRT.LEEAITTRY.LDPKYI.NIL.ENDVITIDLV.NS..QKTQNDVDIADVAYYFEKDVK
RetrocopyQEKNLMILSLRTVLEEAITTRYKLDPKYIINILCENDVITIDLVENSF<QKTQNDVDIADVAYYFEKDVK
ParentalGESLFHSSSMDLRVNGEQLDLDPGQTLIYYVDEKPPEFSMQGLKAGIIAVIVVVIIAVIAGIVVLVISRK
GESLFHSSSMDLRVNGEQLDLDPGQ.LIYYVDE....FSMQGLKAGIIAVIVV..IAVIAGI.VLVISRK
RetrocopyGESLFHSSSMDLRVNGEQLDLDPGQSLIYYVDE----FSMQGLKAGIIAVIVVATIAVIAGI-VLVISRK
ParentalKSMTKYEKAEIKEMGEMHRELNA
K.MTKYEK.EIKEM.EMHR.LNA
RetrocopyKRMTKYEKTEIKEMDEMHRKLNA

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






RNA-Seq - click to see more details

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST - click to see more details

Choloepus hoffmanni was not studied using EST data.

TSS - click to see more details

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab - click to see more details

retro_chof_258 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 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000064741 retrocopy
retro_btau_66,
Choloepus hoffmanni ENSCHOG00000013834 1 retrocopy
retro_chof_258 ,
Callithrix jacchus ENSCJAG000000006241 retrocopy
retro_cjac_3006,
Dasypus novemcinctus ENSDNOG000000117991 retrocopy
retro_dnov_345,
Erinaceus europaeus ENSEEUG000000094621 retrocopy
retro_eeur_151,
Macropus eugenii ENSMEUG000000150742 retrocopies
retro_meug_1984, retro_meug_474,
Microcebus murinus ENSMICG000000001511 retrocopy
retro_mmur_739,
Macaca mulatta ENSMMUG000000123901 retrocopy
retro_mmul_34,
Monodelphis domestica ENSMODG000000010771 retrocopy
retro_mdom_104,
Mus musculus ENSMUSG000000453941 retrocopy
retro_mmus_185,
Ochotona princeps ENSOPRG000000043011 retrocopy
retro_opri_1225,
Pelodiscus sinensis ENSPSIG000000156801 retrocopy
retro_psin_22,
Pan troglodytes ENSPTRG000000119021 retrocopy
retro_ptro_92,
Rattus norvegicus ENSRNOG000000156671 retrocopy
retro_rnor_252,
Sus scrofa ENSSSCG000000084291 retrocopy
retro_sscr_69,
Ictidomys tridecemlineatus ENSSTOG000000086311 retrocopy
retro_itri_106,
Tursiops truncatus ENSTTRG000000042352 retrocopies
retro_ttru_21, retro_ttru_394,


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