RetrogeneDB ID:

retro_chof_18

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_222169:534..1545(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCHOG00000010831
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCHOG00000003275
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_chof_18
CTCTTCCGCCGCCATTTTAAATCCAGCTCCATACAACGCTCCGCTGCCGCCGCTACTGGGACTCGGTCTGCGCGCCAGCA
CCCCCCTACCGACAATTCCGCCACCATGGAGGACATGAACGAGTACAGCAACATAGAGGAATTCGCAGAGGGATCCAAAA
TTAACGCGAGCAAGAATCAGCAGGATGACGGTAAAATGTTTATTGGAGGCTTGAGCTGGAATACAAGCAAGAAAGATCTG
ACTGAATATTTGTCTCGATTTGGAGAGGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGAAGATCAAGAGGATT
TGGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCAAATTGA
TAGACCCCAAAAGGGCGAAGGCTTTAAAAGGGAAAGAACCCCCTAAAAAAGTTTTTGTGGGTGGATTGAGCCCAGATACT
TCTGAAGAGCAAATAAAAGAATATTTTGGAGCATTTGGAGAGATTGAAAATATTGAACTTCGCATGGATACAAAAACAAA
TGAAAGAAGAGGATTTTGTTTTATCACAGATACAGATGAAGAGCCAGTAAAGAAATTATTAGAAAGCAGATACCATCAAA
TTGGTTCTGGAAGGTGTGAAATCAAGGTTGCACAACCCAAAGAGGTATATAGGCAGCAACAGCAACAACAGAAAGGAGGA
AGAGGAGCTGCAGCTGCTGGACGAGGTGGTACAAGGGGTCGAGGGCGAGGTTGGGGCCAAAACTGGAACCAAGGATTTAA
TAACTGTTATGGTCAAGGATACGGAAATTACAATAGTGCCTATGGTGGTGATCAGAACTATAGTGGCTATGGCGGATATG
ATTATACTGGGTATAACTATGGGAACTATGGATATGGACAGGGATATACAGACTACAGTGGCCAACAGAGCACATACGGC
AAGGCATCTCGAGGGGGTGGCAATCACCAAAACAATTACCAGCCATACTAA

ORF - retro_chof_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFRRHFKSSSIQRSAAAATGTRSARQHPPTDSSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
LFRRHFKSSSIQRSAAAATGTRSARQHPPTD.SATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
RetrocopyLFRRHFKSSSIQRSAAAATGTRSARQHPPTDNSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
ParentalLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
LSW.TSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
RetrocopyLSWNTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
ParentalALKGKEPPKKVFGGGLSPDTSEEQIKEYXXXXXXIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESR
ALKGKEPPKKVF.GGLSPDTSEEQIKEY......IENIEL.MDTKTNERRGFCFIT.TDEEPVKKLLESR
RetrocopyALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELRMDTKTNERRGFCFITDTDEEPVKKLLESR
ParentalYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAAGRGGTRGRGRGQGQNWNQGFNNYY-DGYGNYSSA
YHQIGSG.CEIKVAQPKEVYRQQQQQQKGGRGAAAAGRGGTRGRGRG.GQNWNQGFNN.Y..GYGNY.SA
RetrocopyYHQIGSGRCEIKVAQPKEVYRQQQQQQKGGRGAAAAGRGGTRGRGRGWGQNWNQGFNNCYGQGYGNYNSA
ParentalYGGD-NYSGYGGYDYTKYNYGNYG-GQGYTDYSGQQSTYGKASRGGGNHQNNYQPY
YGGD.NYSGYGGYDYT.YNYGNYG.GQGYTDYSGQQSTYGKASRGGGNHQNNYQPY
RetrocopyYGGDQNYSGYGGYDYTGYNYGNYGYGQGYTDYSGQQSTYGKASRGGGNHQNNYQPY

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_18 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 19 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148042 retrocopies
retro_btau_1827, retro_btau_461,
Canis familiaris ENSCAFG000000089401 retrocopy
retro_cfam_1086,
Choloepus hoffmanni ENSCHOG000000001608 retrocopies
retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni ENSCHOG00000003275 2 retrocopies
retro_chof_1578, retro_chof_18 ,
Choloepus hoffmanni ENSCHOG0000001383215 retrocopies
retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Cavia porcellus ENSCPOG000000156195 retrocopies
retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Dipodomys ordii ENSDORG000000009681 retrocopy
retro_dord_145,
Equus caballus ENSECAG000000226921 retrocopy
retro_ecab_1082,
Loxodonta africana ENSLAFG000000086121 retrocopy
retro_lafr_650,
Microcebus murinus ENSMICG000000014454 retrocopies
retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus ENSMLUG000000144522 retrocopies
retro_mluc_1140, retro_mluc_1761,
Mustela putorius furoENSMPUG000000147532 retrocopies
retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys ENSNLEG000000086361 retrocopy
retro_nleu_673,
Oryctolagus cuniculus ENSOCUG000000138051 retrocopy
retro_ocun_505,
Otolemur garnettii ENSOGAG000000025014 retrocopies
retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps ENSOPRG000000071783 retrocopies
retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis ENSPCAG000000115431 retrocopy
retro_pcap_366,
Rattus norvegicus ENSRNOG000000022701 retrocopy
retro_rnor_1365,
Sorex araneus ENSSARG000000099611 retrocopy
retro_sara_421,


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