RetrogeneDB ID:

retro_chof_512

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_11609:6446..7155(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RANBP9
Ensembl ID:ENSCHOG00000006785
Aliases:None
Description:RAN binding protein 9 [Source:HGNC Symbol;Acc:13727]


Retrocopy-Parental alignment summary:






>retro_chof_512
TGGGACAAACATTCCTATGGACACTATGGTGATGATAGGCATCCCTTCTGCTCCTTGGGGACTGGCCATCCCTATGGTTC
CACATTCACCACAGGAGATGTGATTGGCTGCAGTGTCAACCTGATCAAAAGCACCTGCTTCTACACCAAGAATGGCCACA
GCCTTAGTATAGCCTTCACAGACCTCCAGGCCACCCTGTACCCCACTGTAGGCCAACAGATGATAGGGGAGACTGTGGAC
ACCAACTTTGGGCAGCAGCCCTTCCTGTCTGACATTGAGGACTACATGCAGGAGTGGCACATCAAGGTCTAGGGCACTGC
CCACTGTTTCCCCATCAGTGCCTGGCTTGGTGAGTGGCAGACGGTGCTGTAGAACATGGTCTCGTCTTATCTGGTGCACC
ACAGGTATTGTGCCATGGCCATGGCTTTTGCCCAAATGACTGAAACCCTGATTCAGGAAGAACAGGTGTCCATAAAGAAC
AGACAAAAGATCCAAAAGTTGGTGGTGGAGGGCTTGTGGATGAGGCCATTGAGACCACACAGTGCTTCTATCCAGGGCTT
CTGGAGCACAACCTCAACCTGCTCTTTTTGCTGAAGTGCAACAGTTTGTGGAGATGGTGAATGGGACTGACAGTGGCTTG
AGCTCCCAAAGCCCCAATTCTCAGTACAGCTACACTGGTTCCTCCAGCCTCAGCCCCCACATGGCCCCA

ORF - retro_chof_512 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.7 %
Parental protein coverage: 50.21 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalWGKHSYGYHGDDGHSFCSSGTGQPYGPTFYTGDVIGCCVNLINNTCFYP-DGHSLGIAFTDLPPNLYPTV
W.KHSYG..GDD.H.FCS.GTG.PYG.TF.TGDVIGC.VNLI..TCFY...GHSL.IAFTDL...LYPTV
RetrocopyWDKHSYGHYGDDRHPFCSLGTGHPYGSTFTTGDVIGCSVNLIKSTCFYTKNGHSLSIAFTDLQATLYPTV
ParentalGLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQAQIDRFPIGEREGEWQTMIQKMVSSYLVHHGYCATA
G.Q..GE.VD.NFGQ.PF..DIEDYM.EW..K.......FPI....GEWQT....MVSSYLVHH.YCA.A
RetrocopyGQQMIGETVDTNFGQQPFLSDIEDYMQEWHIKV*GTAHCFPISAWLGEWQTVL*NMVSSYLVHHRYCAMA
ParentalEAFARSTDQTVLEELASIKNRQRIQKLVL-AGRMGEAIETTQQLYPSLLERNPNLLFTLK-VRQFIEMVN
.AFA..T.....EE..SIKNRQ.IQKLV...G...EAIETTQ..YP.LLE.N.NLLF.LK.V.QF.EMVN
RetrocopyMAFAQMTETLIQEEQVSIKNRQKIQKLVV<GGLVDEAIETTQCFYPGLLEHNLNLLFLLK<VQQFVEMVN
ParentalGTDSEVRCLGGRSPKSQDSYPVSPRPFSSPSMSP
GTDS....L...SP.SQ.SY..S.....SP.M.P
RetrocopyGTDSG---LSSQSPNSQYSYTGSSS--LSPHMAP

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_512 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 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000006785 2 retrocopies
retro_chof_1695, retro_chof_512 ,
Callithrix jacchus ENSCJAG000000197971 retrocopy



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