RetrogeneDB ID:

retro_chof_263

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_5800:14352..15130(+)
Located in intron of:ENSCHOG00000012810
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GLCCI1
Ensembl ID:ENSCHOG00000012559
Aliases:None
Description:glucocorticoid induced transcript 1 [Source:HGNC Symbol;Acc:18713]


Retrocopy-Parental alignment summary:






>retro_chof_263
CAAAATCATGTTTCACGTGTACCCTGCAATGTAGAAGGAATTAAGTCCTGAATTAGAAAAGGTATTCATTAAAGAAAATA
ACAGGAAGGAGGAAGTGACCAAGCCTTTGGACATACCAGATGGCCGAAGAGCTCCCCTCCGTGCTCACTACCAGAGCAGT
AGGCCTCGCAGCACTGACACTGACTCCCTCTGTCCAGGAGTGCAGCAGCAGCTGCAGCGGTAATTCACCCTGTGTCTCCC
CATTTTGTCCCCCGGAATCCCAGGATGGCAGCCCTTGCTCAACTGAAGATTTGCCCTATGATCATGATAAAGACAGTGGG
AGTAGCTCACCATTACCCAAGAATGCTTCATCTCCCAAACCAAACAACAGCTACATGTCAAACGGGAGCCCCCGGAGGGA
TGTGAGCAAGTGAAGGTCTTTCAGGAAATGGTGTCTGGTCAGCCTATCTCAGTCCTTCTCTTTTCATGTCCTGACAAAAA
CAAGGTTAATTTCATCCCAGCTGGTTCAGCTTTCTGTCCTGTAAAAGTTCTAGGCCCTCTCTTACCTGCCTCCGACCTGA
TGCTCAAGAACTCTCCTAACTCTGGCCAGACCTCAGCTCTGGCCACTCTGACTGTTGAACAGCTCTCACCCTGGGTTTCC
TTTGCATCTCCTTCCAATGACACCAGCACAGTGGGTCCCACAGAGGTCTCTACTCAACAGCCATCCCAGCAGCAGCAGCA
GCTTCTGCAGGAACTGCAGGCTGAAGAGCTCATCTCTGCTCAGAACTATGTGATCATC

ORF - retro_chof_263 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.55 %
Parental protein coverage: 65.82 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKSSVSRVSCNVEGI-SPELEKVFIKENNGKEEVTKPLDIPDGRRAPLPAHYRSSSTRSIDTQT-PSVQER
...VSRV.CNVEGI.SPELEKVFIKENN.KEEVTKPLDIPDGRRAPL.AHY.SS..RS.DT...P.....
RetrocopyQNHVSRVPCNVEGI>SPELEKVFIKENNRKEEVTKPLDIPDGRRAPLRAHYQSSRPRSTDTDS<PLSRSA
ParentalSSSCSSHSPCVSPFCP-PESQDGSPCSAEDLLYDRDKDSGSSSPLPKYASSPKPNNSYM-FKREPPEGCE
........P....F.P.PESQDGSPCS.EDL.YD.DKDSGSSSPLPK.ASSPKPNNSYM..KREPPEGCE
RetrocopyAAAAAVIHPVSPHFVP<PESQDGSPCSTEDLPYDHDKDSGSSSPLPKNASSPKPNNSYM<VKREPPEGCE
ParentalRVKVFEEMASRQPISAPLFSCPDKNKVNFIPTGSAFCPVKLLGPLLPASDLMLKNSPNSGQSSALSTLTV
.VKVF.EM.S.QPIS..LFSCPDKNKVNFIP.GSAFCPVK.LGPLLPASDLMLKNSPNSGQ.SAL.TLTV
RetrocopyQVKVFQEMVSGQPISVLLFSCPDKNKVNFIPAGSAFCPVKVLGPLLPASDLMLKNSPNSGQTSALATLTV
ParentalEQLSSRVSFASLSNDTSTVGPTESSTQQPSQQQQQLLQELQAEEHISAQNYVII
EQLS..VSFAS.SNDTSTVGPTE.STQQPSQQQQQLLQELQAEE.ISAQNYVII
RetrocopyEQLSPWVSFASPSNDTSTVGPTEVSTQQPSQQQQQLLQELQAEELISAQNYVII

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_263 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 2 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000012559 1 retrocopy
retro_chof_263 ,
Mus musculus ENSMUSG000000296381 retrocopy



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