RetrogeneDB ID:

retro_chof_1883

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_413698:204..566(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HDHD1
Ensembl ID:ENSCHOG00000001318
Aliases:None
Description:haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]


Retrocopy-Parental alignment summary:






>retro_chof_1883
ATCTTGCAGCTTCCAATGACCAAAGAGGCACTGGCGGAAGAAAGCGAAATGTTTAAACAGCTGTTCTCCATGGCTGCCGT
GTTGCCAGGTGTCAAAAAATTCACCCACTACCTACAAAAACACAACACACCTTTTGCTCTTGCTCCAAGCTCAGGGTCCA
CATCATTTGAAATGAAAACAAATACATAAAAAGAGTTCTTCAGTTTATTTCACCATATCGTTTTGGGAAATGATCCTGAA
GTGATGAGTGGCAAACCAAATCCTGCCACATATCTAACGTGCGTGAAGATATTTTCTCCTTTGCTCCTGTGGAGAAGTTC
CTGGTGTTTGAAGATGCCCCCAATGGGGTGGAGGTGGCCCTG

ORF - retro_chof_1883 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.36 %
Parental protein coverage: 74.39 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVLQLPVTKEELVEESQTKLKQLFPTAALLPGVEKLIHHLRKYNIPFALATSSGSASFEMKTSSHKEFFSL
.LQLP.TKE.L.EES....KQLF..AA.LPGV.K..H.L.K.N.PFALA.SSGS.SFEMKT...KEFFSL
RetrocopyILQLPMTKEALAEESEM-FKQLFSMAAVLPGVKKFTHYLQKHNTPFALAPSSGSTSFEMKTNT*KEFFSL
ParentalFHHIVLGDDPEVTSGKPDPAIFLTCAKRFSP-SAPVEKCLVFEDAPNGVEAAL
FHHIVLG.DPEV.SGKP.PA..LTC.K.FSP..APVEK.LVFEDAPNGVE.AL
RetrocopyFHHIVLGNDPEVMSGKPNPATYLTCVKIFSP<FAPVEKFLVFEDAPNGVEVAL

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_1883 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 20 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000046161 retrocopy
Choloepus hoffmanni ENSCHOG00000001318 5 retrocopies
Homo sapiens ENSG000001300212 retrocopies
Gorilla gorilla ENSGGOG000000044251 retrocopy
Microcebus murinus ENSMICG000000170821 retrocopy
Macaca mulatta ENSMMUG000000173771 retrocopy
Monodelphis domestica ENSMODG000000175052 retrocopies
Pongo abelii ENSPPYG000000201052 retrocopies
Pteropus vampyrus ENSPVAG000000111491 retrocopy
Tarsius syrichta ENSTSYG000000132384 retrocopies



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