RetrogeneDB ID:

retro_chof_209

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_453:114094..114677(+)
Located in intron of:ENSCHOG00000012973
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:T
Ensembl ID:ENSCHOG00000006236
Aliases:None
Description:T, brachyury homolog (mouse) [Source:HGNC Symbol;Acc:11515]


Retrocopy-Parental alignment summary:






>retro_chof_209
TATTCTCAGTTGGGGAGATGCTTATTCCTGGAACCAGTCCATTGGTTCCACCTTCCAGCCCCTACCCTTGTTTGGAGGTT
CTGCCTCCCTCTCCTCCCTGCATGACTGTGAAAGATAGCTCAACCTGCGAAACTACATCTCAACCCTGTACCCCAGTCCA
TACACTCATCAAAACAGCTCTCCAACCTTTCTGACAATTCATCTGCATGTTTAGGCATGCTCCAATTTCATGACAGTTGG
TCCAGCCTTGGGGTGCCTGCCCAAACCAGCATGCTACTCCTGAGCCATAGCACAGATCCACCCCCTGGTTCTAGTCAGTA
CCTCAACCGGTGGTCTGTGAGTTAACAGCACCATCACTCCTGGCTCCCAGAAGCCAGGGATGTCCAGTGGGCTGGGAGTT
CAGTTCTCTCTAGGCTCCACAGTGCACTGTGCACCCCTTGCCCACATGGTCTCTGCTTCCTCTTCCTCAGGGCCCCTGCT
GTGTGAAGGGGGCACATGCCACAGACATTCCTGTAGCCAGTACAATGCCTTGGCACAAACCTGCCTCACAGCCTCACGGA
CGCCCTTGTTGCCATGTTCCATG

ORF - retro_chof_209 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64. %
Parental protein coverage: 53.28 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalYSQ-WG-WLIPSTSPLCPPASPHP-QFGGSLPLSSPHGCERYPALRSHRSTPYPSPYAHRNNSPTY-SDS
YSQ.WG..LIP.TSPL.PP.SP.P..FGGS..LSS.H.CER...LR...ST.YPSPY.H.N.SPT..SD.
RetrocopyYSQ>WG>MLIPGTSPLVPPSSPYP<LFGGSASLSSLHDCER*LNLRNYISTLYPSPYTHQNSSPTF<SDN
ParentalSSACLSMLQSHDNWSSLGMPAHPSMLPMSHNPSPPTGSSQYPNLWPVS-NGTITPGSQTPGMSNGLGTQF
SSACL.MLQ.HD.WSSLG.PA..SML..SH...PP.GSSQY.N.W.VS.N.TITPGSQ.PGMS.GLG.QF
RetrocopySSACLGMLQFHDSWSSLGVPAQTSMLLLSHSTDPPPGSSQYLNRWSVS>NSTITPGSQKPGMSSGLGVQF
ParentalFRGSTAHYAPLTHTVPASSSSGSPLYEGGATATDIPDSQYDASAQARLIASWTPVSPPSM
..GST.H.APL.H.V.ASSSSG..L.EGG.T......SQY.A.AQ..L.AS.TP..P.SM
RetrocopySLGSTVHCAPLAHMVSASSSSGPLLCEGG-TCHRHSCSQYNALAQTCLTASRTPLLPCSM

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_209 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 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000006236 1 retrocopy
retro_chof_209 ,
Choloepus hoffmanni ENSCHOG000000103871 retrocopy
Equus caballus ENSECAG000000079941 retrocopy
Microcebus murinus ENSMICG000000161221 retrocopy
Nomascus leucogenys ENSNLEG000000115521 retrocopy



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