RetrogeneDB ID:

retro_chof_1388

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_279464:311..951(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNX7
Ensembl ID:ENSCHOG00000008131
Aliases:None
Description:sorting nexin 7 [Source:HGNC Symbol;Acc:14971]


Retrocopy-Parental alignment summary:






>retro_chof_1388
GAAAAGTTTATAGTGAAAAGAATGGTGGAACACTTTAATGATGACTTCACTGAGACACACAGGAATGCATTACATAAGTT
TTTTGAACCAAACTGCCGATCATCCAACTTTAACATTTAATGAAGACTTCAAAGTTTTTCTTACTGCACAAGCTTGGAAA
CTCTCTTCTCATAAGAAGCAAGGGTCTGGGCTGCTAAGTTGGATGGGGGAAACAGTAAGAGCTGTTGCATCCTCAATGAG
AGGATTTAAAAATCGCCCAGAGGAATTCATGGATACAGATAATTTTATTGAAACATTTAGCCAGAAAACAAACTTGATAG
GTAAAATATCACAGAATTTACATGAAAGAAAGGGAATATTTTGATGAAATGAAAGAATATGGCCCAATTCATATTCTGTG
GTTGGCATCAGAAGAGGATCCAGTAGACAACCTAAAGGTGCTGCCAGCTGCATTGGTAAATGCTGTAAGGCCACTGAAAA
ACAGGTGTCTGGACTCTCAGAAGCCCTACTTCCTGTTGTACATGAGTATGTGCATTATAGTGAAATGTTAATGGGTGCTT
TGAAAAGAAGAGACCAAATATAAGCAGAACTGGATTCCAAAGTTGAAGCTTTGAACTATAAAAAGGCACATACTGATCTG

ORF - retro_chof_1388 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.49 %
Parental protein coverage: 73.04 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEKFIVKGMVERFNDDFIETRRKALHKF-LNRIADHPTLTFNEDFKVFLTAQAWELSSHKKHGPGLLSRMG
EKFIVK.MVE.FNDDF.ET.R.ALHKF.LN..ADHPTLTFNEDFKVFLTAQAW.LSSHKK.G.GLLS.MG
RetrocopyEKFIVKRMVEHFNDDFTETHRNALHKF>LNQTADHPTLTFNEDFKVFLTAQAWKLSSHKKQGSGLLSWMG
ParentalQTVRAVASSMRGVKNRPEEFMDMNNFIETFSQKINLIDKISQRIY-KEEREYFDEMKEYGPIHILWSASE
.TVRAVASSMRG.KNRPEEFMD..NFIETFSQK.NLI.KISQ....KE.REYFDEMKEYGPIHILW.ASE
RetrocopyETVRAVASSMRGFKNRPEEFMDTDNFIETFSQKTNLIGKISQNLH>KE-REYFDEMKEYGPIHILWLASE
ParentalEDLVDTL-KGVASCIDRCCKATEKQMSGVSEALLPVVHEYVLYSEMLMGVMKRRDQIQAELDSKVEALNY
ED.VD.L.KG.ASCI..CCKATEKQ.SG.SEALLPVVHEYV.YSEMLMG..KRRDQI.AELDSKVEALNY
RetrocopyEDPVDNL<KGAASCIGKCCKATEKQVSGLSEALLPVVHEYVHYSEMLMGALKRRDQI*AELDSKVEALNY
ParentalRKADTDL
.KA.TDL
RetrocopyKKAHTDL

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_1388 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 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000314611 retrocopy
Choloepus hoffmanni ENSCHOG00000008131 2 retrocopies
retro_chof_1097, retro_chof_1388 ,
Gorilla gorilla ENSGGOG000000235771 retrocopy
Macropus eugenii ENSMEUG000000113201 retrocopy
Sarcophilus harrisii ENSSHAG000000024871 retrocopy
Tupaia belangeri ENSTBEG000000001681 retrocopy



Copyright © RetrogeneDB 2014-2017