RetrogeneDB ID:

retro_chof_1033

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_187534:1726..2554(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GPD1L
Ensembl ID:ENSCHOG00000012633
Aliases:None
Description:glycerol-3-phosphate dehydrogenase 1-like [Source:HGNC Symbol;Acc:28956]


Retrocopy-Parental alignment summary:






>retro_chof_1033
GTTGCTGTCTCAAATCTCAGCGAGGCAGTGCAGGATGCAGACCTGCTGGTGTTTGTCATTCCTCACCAGTTCATTCACAG
AATCTGTGATGAGATTACTGGAAGGGTGCCCAAAGAAGCGCTAGGAATCACCCTCATCAGGGGGATAGACCAGGGCCCTG
AGGGGCTGAAACTCATTTCCGACATCATCCGAGAGAAGACGAGCATTGACATCAGTGTGCTGATGGGAGCCAACATTGCC
AACAAGGTGGCTGCAGACAAGTTCTGTGAGACCACCATCGGCAGCAAAGTAATGGAGAATGGCCTTCTCTTCAAAGAACT
TCTGCAGACTCCAAATTTTCGAATTACTGTGGTTGATGATGCAGATACTGTTGAACTTTGTGGTGCTCTTAAGAACGTTG
TGGCTGTAGGAGCTGGGTTCTGCGATGGCCTCCACTGTGGAGACAACACCAAAGCCTCTGTCATCTGCCTGGGCCTCATG
AAAATGATTGCATTTGCCAAGATCTTCTGCAATGGCCATGTGTCCACAGCCACCTTCCTGGAGAGCTGTGGGATGGCTGA
CCTGATCACCACCTGCTACGGAGGCCGGAACCGCAGGGTGGCCGAGGCGTTCGCCAGGACTGGAAAGACCATTGAAGAAC
TGGAGAACGAGGTGCTGAATGGGCAGAAACTCCAAGGACCTCAGACTTCTGCTGAAGTGTACCACATCCTCAAACAGAAG
GGCCTAGTTGACAAGTTTCCATTGTTTACTGCAGTGTATCAGATCTGCTAGGAAGGAAAATCGGTTCAAGATATGTTGTC
TTGTCTCCAGAGTCATCCAGAGCATAGA

ORF - retro_chof_1033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.2 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLIKGIDKGPEGLKLISDIIREKMGID
VAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLI.GID.GPEGLKLISDIIREK..ID
RetrocopyVAVSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKEALGITLIRGIDQGPEGLKLISDIIREKTSID
ParentalISVLMGANIANEVAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF
ISVLMGANIAN.VAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF
RetrocopyISVLMGANIANKVAADKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNVVAVGAGF
ParentalCDGLRCGDNTKAAVIRLGLMEMIAFAKIFCKGHVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKT
CDGL.CGDNTKA.VI.LGLM.MIAFAKIFC.GHVSTATFLESCG.ADLITTCYGGRNRRVAEAFARTGKT
RetrocopyCDGLHCGDNTKASVICLGLMKMIAFAKIFCNGHVSTATFLESCGMADLITTCYGGRNRRVAEAFARTGKT
ParentalIEELENEMLNGQKLQGPQTSAEVYRILKQKGLVDKFPLFTAVYQICYEGKSVQDMLSCLQSHPQHK
IEELENE.LNGQKLQGPQTSAEVY.ILKQKGLVDKFPLFTAVYQIC.EGKSVQDMLSCLQSHP.H.
RetrocopyIEELENEVLNGQKLQGPQTSAEVYHILKQKGLVDKFPLFTAVYQIC*EGKSVQDMLSCLQSHPEHR

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_1033 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 10 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000098261 retrocopy
Choloepus hoffmanni ENSCHOG00000012633 5 retrocopies
Loxodonta africana ENSLAFG000000139961 retrocopy
Microcebus murinus ENSMICG000000110601 retrocopy
Mus musculus ENSMUSG000000506273 retrocopies
Oryctolagus cuniculus ENSOCUG000000100932 retrocopies
Otolemur garnettii ENSOGAG000000132431 retrocopy
Procavia capensis ENSPCAG000000161321 retrocopy
Rattus norvegicus ENSRNOG000000264552 retrocopies
Sus scrofa ENSSSCG000000219771 retrocopy



Copyright © RetrogeneDB 2014-2017