RetrogeneDB ID:

retro_chof_1971

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_438816:19..649(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM60A
Ensembl ID:ENSCHOG00000007193
Aliases:None
Description:family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]


Retrocopy-Parental alignment summary:






>retro_chof_1971
TTTGGTTTTCACAAGCCAAAGATGTACTAAAGTACAGAGAGCTGCTGTATTTGCAGGGCTAAGTCCTCTGGTTCTCCATC
TGTGGACAGTAAATGCTATGAAAAGAACTTCCAGAGTTGTTTTGGGTTGCATGAGACTTGTTCAGGAGATAGCTGCAATG
CCTATGTCCTATTTGTGAAAAAGATGGAAGAAGTTGCCAGTAGGATCAAAACAAACAAACAAACCTGCAATCTTGTGGCA
GATACAAGAACAGGAAAGACTACATTGAATCCAAAGAAAGTGAAAATTCCGTCTGGAAATAAGATAAAAAGCAACCAGAT
CAGTAAAATGAAGAAAGAATTTAAACTGCACAATTCTGATGGTCACAGTGCCACCTCAAGTGCCTCTCCAGTCTAATCTC
CTTGTTAGGTTATGTCAGATGATAGCTCAGATGGAGAGATGGCTTTTTGCTCTAACAGAATACCAGTCTTTTCCTTTTTA
GATCTTACGTACTTGAAAAGACAGAAAATATGTTGTGGGATTATCTATAAAGGCCGTTTTGGGAAAGTGCTCATCGACAC
ACATCTATTCAAGCCTTGCTGCAGTAATCAGAAAGCAGCTGTTGAGACGTTGGAGGAGCAGGGGCCAGAC

ORF - retro_chof_1971 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.22 %
Parental protein coverage: 95.48 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGSK
FGFHKPKMY.S.E.CCICRAKSS.S...DSK.YEK.FQSCFGLHET.SGD.CNA.VL.VK.........K
RetrocopyFGFHKPKMY*STESCCICRAKSSGSPSVDSKCYEKNFQSCFGLHETCSGDSCNAYVLFVKKMEEVASRIK
ParentalKN---WNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQKEFKRHXXXXXXXTSSASPAQSPCYS
.N....N.V.D.R.G...KTTL.PKKVK..SGN.IKSNQISK..KEFK.H.......TSSASP..SPC..
RetrocopyTNKQTCNLVADTRTG---KTTLNPKKVKIPSGNKIKSNQISKMKKEFKLHNSDGHSATSSASPV*SPC*V
ParentalNQSDDGSDTEMASGSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSNKKTTAEKPEE
..SDD.SD.EMA..SNR.PVFSFLDLTY.KRQKICCGIIYKGRFG.VLIDTHLFKPCCSN.K...E..EE
Retrocopy-MSDDSSDGEMAFCSNRIPVFSFLDLTYLKRQKICCGIIYKGRFGKVLIDTHLFKPCCSNQKAAVETLEE
ParentalQGPE
QGP.
RetrocopyQGPD

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_1971 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 60 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000011611 retrocopy
retro_btau_1020,
Canis familiaris ENSCAFG000000106854 retrocopies
retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni ENSCHOG00000007193 17 retrocopies
retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971 , retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus ENSCJAG000000012153 retrocopies
retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Felis catus ENSFCAG000000089554 retrocopies
retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Homo sapiens ENSG000001391463 retrocopies
retro_hsap_1928, retro_hsap_1945, retro_hsap_4029,
Gorilla gorilla ENSGGOG000000154843 retrocopies
retro_ggor_1405, retro_ggor_1415, retro_ggor_2704,
Myotis lucifugus ENSMLUG000000098273 retrocopies
retro_mluc_1663, retro_mluc_1672, retro_mluc_765,
Macaca mulatta ENSMMUG000000091552 retrocopies
retro_mmul_1074, retro_mmul_2324,
Mus musculus ENSMUSG000000399854 retrocopies
retro_mmus_1234, retro_mmus_1471, retro_mmus_1557, retro_mmus_3331,
Nomascus leucogenys ENSNLEG000000164871 retrocopy
retro_nleu_1213,
Oryctolagus cuniculus ENSOCUG000000086181 retrocopy
retro_ocun_1176,
Otolemur garnettii ENSOGAG000000089274 retrocopies
retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Pongo abelii ENSPPYG000000043962 retrocopies
retro_pabe_1592, retro_pabe_3309,
Rattus norvegicus ENSRNOG000000460481 retrocopy
retro_rnor_2858,
Rattus norvegicus ENSRNOG000000499432 retrocopies
retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii ENSSHAG000000062611 retrocopy
retro_shar_670,
Ictidomys tridecemlineatus ENSSTOG000000070971 retrocopy
retro_itri_16,
Tursiops truncatus ENSTTRG000000084653 retrocopies
retro_ttru_1162, retro_ttru_1498, retro_ttru_984,


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