RetrogeneDB ID:

retro_chof_974

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_179011:2764..3392(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TRA2A
Ensembl ID:ENSCHOG00000001130
Aliases:None
Description:transformer 2 alpha homolog (Drosophila) [Source:HGNC Symbol;Acc:16645]


Retrocopy-Parental alignment summary:






>retro_chof_974
AGTGACAACAGCGAGCAGAACTACCACAGAACTTCTGGTTCCAGAAGTGGAAGTGCTCATGGATCTGAGAAATCTGCAGG
GCATACCCCTGCAAGGTCTCACTCCAAGGAAGATTCCAGGTGTTCCACATCAAAGCCCAGGTCCAAATATGAATCTAGGT
CTAGATCCAGAAGAATTTCTTGAAGAAATTACACAAGGTCATGGCCTCAGTACAGCTCTCATAGATGAACATGTAGCAGG
TTTTACAGTCGAGATTATCACAGACCGCATAGCCATAGTCATTCTCCAATGTCTACTCACAGGCTATGAGGTTGGAAATT
GGGCAAATCTTGATCCCATCAGTTGCCTTGGAGTATTTTGGTTGAGCTTGTACACCATAGAAAGAAATTTAAGAGAAGTG
TTCTCTAAATATGGCCCCATTGCTGACATGTCTATTGCATATGACCAGCAGTCTAGACTTCAAAAGGATTTTGCCTTTGT
GTATTTTGAAAATGTAGATGATTCCAAGGAAGCTAAAGTGTATGCCAATGAAATGGAGCTTGATGGGCATAGGATCAGAG
TTCATTTCTCTATAACTAAAAGATGGCATACCCCAACACCAGGAATTTACATGCAGAGACCTACCTAT

ORF - retro_chof_974 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.88 %
Parental protein coverage: 75.53 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSEVEENNFEGRESRSQSKSPTGTPARVKSESRSGSRSPSRV-SKHSESHSRSRSKSRSRSRRHSHRRYTR
S...E.N...R.S.S.S.S..G.....KS......RS.S...S..S.S..RS...SRSRSRR.S.R.YTR
RetrocopySDNSEQNYH-RTSGSRSGSAHGSE---KSAGHTPARSHSKEDSRCSTSKPRSKYESRSRSRRIS*RNYTR
ParentalSRSHSHSHRRRSRSRSYTPEYRRRRSRSHSPMSNRRR-HTGSRANPDPNTCLGVFGLSLYTTERDLREVF
S.....SHR....SR.Y...Y.R..S.SHSPMS..R....G..AN.DP..CLGVF.LSLYT.ER.LREVF
RetrocopySWPQYSSHR*TC-SRFYSRDYHRPHSHSHSPMSTHRL>EVGNWANLDPISCLGVFWLSLYTIERNLREVF
ParentalSRYGPLSGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITKRAHTPTPGIYM
S.YGP.......YDQ.......FAFVYFE..DDSKEA...AN.MELDG.RIRV..SITKR.HTPTPGIYM
RetrocopySKYGPIADMSIAYDQQSRLQKDFAFVYFENVDDSKEAKVYANEMELDGHRIRVHFSITKRWHTPTPGIYM
ParentalGRPTH
.RPT.
RetrocopyQRPTY

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_974 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 12 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000001130 1 retrocopy
retro_chof_974 ,
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
Callithrix jacchus ENSCJAG000000015091 retrocopy
Echinops telfairi ENSETEG000000072502 retrocopies
Homo sapiens ENSG000001645481 retrocopy
Gorilla gorilla ENSGGOG000000090531 retrocopy
Mustela putorius furoENSMPUG000000134801 retrocopy
Nomascus leucogenys ENSNLEG000000147941 retrocopy
Otolemur garnettii ENSOGAG000000097333 retrocopies
Pongo abelii ENSPPYG000000177281 retrocopy
Pan troglodytes ENSPTRG000000189881 retrocopy
Sorex araneus ENSSARG000000129001 retrocopy



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