RetrogeneDB ID:

retro_chof_11

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_12310:4..3022(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCHOG00000003932
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000006061
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_11
ACGCCTAGCGCAATGGCGGCGGCCGCGGCGGAGCAGCAACAGTTCTACCTGCTCCTGGGAAACCTGCTCAGCCCCGACAA
TGTGGTCCGGAAACAGGCAGAGGAAACCTATGAGAATATCCCAGGCCAGTCAAAGATCACATTCCTCTTACAAGCCATTA
GAAATACAACAGCTGCTGAGGAGGCTAGACAAATGGCTGCCGTTCTCCTAAGACGTCTTTTGTCCTCTGCATTTGATGAA
GTCTATCCAACTCTTCCTTCTGATGTTCAGACTGCCATCAAGAGTGAGCTACTAATGATTATTCAGATGGAAACACAATC
TAGCATGAGGAAAAAAATTTGTGATATTGCTGCAGAACTGGCCAGGAATTTAATAGATGAGGATGGCAACAATCAGTGGC
CTGAAGGTTTGAAGTTCCTTTTTGATTCAGTTAGCTCTCAAAATGTAGGACTGCGGGAAGCTGCCCTTCATATTTTCTGG
AATTTTCCTGGAATTTTTGGGAATCAACAGCAGCACTATTTAGACGTCATCAAACGGATGTTAGTTCAGTGTATGCAAGA
TCAGGAACATCCATCGATCAGGACATTATCTGCTAGAGCTACAGCTGCATTTATACTTGCAAATGAGCATAATGTTGCTC
TGTTCAAACATTTTTCAGACTTATTACCTGGATTCTTACAGGCTGCAAATGATTCATGCTACCAGAACGACGATTCAGTC
CTAAAATCTCTTGTTGAGATTGCAGATACCGTTCCAAAGTATTTGCGTCCTCATTTAGAAGCCACTCTACAGCTAAGTCT
AAAGTTATGCGGAGACACTAGTCTCAATAATATGCAATGCCAGATTGCCCTTGAAGTAATCGTGACCCTGTCTGAGACAG
CAGCTGCTATGTTAAGAAAACATACCAATATTGTTGCACAGACTATTCCTCAGATGTTAGCAATGATGGTTGATCTGGAA
GAGGATGAGGATTGGGCAAATGCTGATGAACTAGAAGATGATGATTTTGACAGCAATGCAGTTGCTGGTGAGAGTGCTTT
AGACCAAATGGCTTGCGGACTTGGTGGAAAACTTGTTCTACCAATGATCAAGGAACACATTATGCAAATGCTTCAAAATC
CTGACTGGAAATACCGGCATGCAGGATTGATGGCTTTGTCTGCCATTGGTGAAGGATGCCACCAGCAAATGGAAGGGATT
CTAAATGAGATAGTAAATTTTGTTTTGCTTTTTCTTCAGGATCCTCATCCAAGAGTAAGGTATGCAGCCTGTAATGCTGT
GGGACAGATGGCTACAGATTTTGCACCTGGATTCCAAAAGAAATTCCATGAGAAGGTGATTGCAGCTCTGTTGCAGACAA
TGGAAGACCAAGGCAATCAACGGGTACAGGCCCATGCAGCTGCTGCGCTCATTAATTTTACTGAAGACTGTCCCAAGTCA
CTACTGATTCCATATTTAGACAATTTGGTGAAACATTTGCATTCCATTATGGTACTGAAACTTCAAGAGTTGATTCAAAA
AGGCACCAAGTTAGTTTTGGAACAAGTTGTGACATCCATTGCATCAGTTGCAGATACCGCAGAAGAAAAATTTGTCCCCT
ACTATGATTTATTTATGCCATCACTAAAGCATATTGTTGAGAATGCAGTTCAGAAGGAACTCAGACTTCTGAGAGGAAAA
ACTATTGAATGCATCAGCCTCATTGGTCTGGCTGTTGGGAAAGAAAAATTCATGCAAGATGCTTCAGATGTGATGCAGCT
ATTACTGAAGACTCAGACAGACTTCAATGATATGGAAGATGATGAACCTCAGATTTCTTACATGATCTCAGCGTGGGCCA
GAATGTGCAAAATCCTTGGAAAAGAATTTCAGCAATACCTTCCAGTGGTTATGGGGCCTTTAATGAAGACAGCTTCAATT
AAACCCGAAGTAGCACTTTTAGATACCCAAGACATGGAGAATATGAGTGATGATGATGGTTGGGAATTTGTGAACCTTGG
AGATCAGCAAAGTTTTGGTATTAAAACTGCAGGGCTGGAAGAAAAGTCAACTGCTTGCCAGATGCTGGTTTGCTATGCTA
AGGAGTTAAAGGAAGGCTTTGTGGAATACACTGAACAAGTTGTAAAACTGATGGTCCCTTTACTGAAATTTTATTTCCAT
GATGGTGTTCGAGTGGCAGCAGCAGAATCCATGCCTCTTCTCCTGGAATGTGCAAGAGTTCGTGGTCCTGAGTATCTCAC
ACAGATGTGGCATTTTATGTGCGATGCTCTAATCAAGGCCATTGGCACAGAACCAGATTCAGATGTCCTGTCAGAAATAA
TGCATTCTTTTGCAAAGTGCATTGAAGTAATGGGAGATGGATGCCTTAATAATGAACACTTTGAAGAACTGGGAGGTATA
TTGAAAGCAAAACTTGAAGAACATTTTAAAAATCAAGAATTGCGACAAGTTAAAAGACAAGATGAAGACTATGATGAACA
GGTTGAAGAGTCACTACAAGATGAGGATGATAATGATGTATATATTCTGACCAAAGTGTCAGACATTTTACACTCAATAT
TCAGTAGCTACAAGGAAAAAGTGTTACCATGGTTTGAACAGCTGCTTCCTTTAATTGTCAACCTAATTTGTCCACATAGA
CCATGGCCAGACAGACAGTGGGGATTGTGCATCTTTGATGATGTAATAGAACACTGTAGTCCAGCCTCATTTAAATATGC
AGAATATTTCTTAAGGCCAATGCTCCAATATGTATGTGACAATAGCCCAGAAGTCAGACAAGCTGCTGCATATGGCCTAG
GAGTCATGGCACAGTATGGTGGAGATAACTATCGTCCTTTTTGTACAGAAGCACTTCCCCTGCTGGTAAGAGTTATTCAG
TCTGCAGATTCTAAGACCAAAGAAAATGTCAATGCTACAGAGAACTGCATTTCAGCAGTAGGGAAGATAATGAAATTCAA
ACCTGACTGTGTAAATGTTGAAGAAGTCCTACCACACTGGTTATCGTGGCTCCCACTG

ORF - retro_chof_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.14 %
Parental protein coverage: 51.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
ETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
RetrocopyETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
ParentalTQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNVGLREAALHIFWNFPGIFGNQQQHYL
TQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNVGLREAALHIFWNFPGIFGNQQQHYL
RetrocopyTQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNVGLREAALHIFWNFPGIFGNQQQHYL
ParentalDVIKRMLVQCMQDQEHPSIRTLSARTTAAFIL-NEHNVAXXXXXXXXXXXXXXAVNDSCYQNDDSVLKSL
DVIKRMLVQCMQDQEHPSIRTLSAR.TAAFIL.NEHNVA..............A.NDSCYQNDDSVLKSL
RetrocopyDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFSDLLPGFLQAANDSCYQNDDSVLKSL
ParentalVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
VEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQ.Q.ALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
RetrocopyVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQCQIALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
ParentalMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
MMVDLEEDEDWANADELEDDDFDSNAVAGESALD.MACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
RetrocopyMMVDLEEDEDWANADELEDDDFDSNAVAGESALDQMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
ParentalALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
ALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
RetrocopyALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
ParentalEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDSLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
EDQGNQRVQAHAAAALINFTEDCPKSLLIPYLD.LVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
RetrocopyEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
ParentalDTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
DTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
RetrocopyDTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
ParentalFNDMEDDDPQ
FNDMEDD.PQ
RetrocopyFNDMEDDEPQ

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_11 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 21 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG000000393741 retrocopy
retro_btau_104,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG00000006061 1 retrocopy
retro_chof_11 ,
Cavia porcellus ENSCPOG000000048272 retrocopies
retro_cpor_265, retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG000000161901 retrocopy
retro_lafr_22,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG000000306622 retrocopies
retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys ENSNLEG000000078312 retrocopies
retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,




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