RetrogeneDB ID:

retro_chof_1178

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_218846:80..557(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSCHOG00000013843
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_chof_1178
GAAGAGGCAGAGCCTGAAGAATTTGTGGTGGAAAAAAGTACTGGATCGACGTGTAGCTAATGGGAAGGTGGAGTATTTCT
TGAAGTGGAAGGGATTTGCAGATGCTGACAATACTTGGGAGCCTGAAGAGAATTTAGATCACCCAGAGTTAATTGAAGAA
TTTCTTAATTCTCAAAAAGCTGGTAAAGAAAAAGATGGTACAACAAGAAAATCTTTATCTGACAGTGAATCTGAAGACAG
CAAATCTAAGAAGAGATGCTGCTGACAAACCGAGAGGCTTTGCTAGAGGTCTTGATCCTGAATGCATGATTGGTGCCACA
GACAGCAGTGGAGAATTAATGTTTCTCAAGAAACGGAGAGATTCAGATGAGGCAGACTTGGGGCTGTCAGAGGGGCAAAC
AGGAAGTGTCCTCAAATTGTAGTTGCTTTTTATGAAGCGAGACTAACTAGCATTCTTGTCCAGATGATGAAGCTCAA

ORF - retro_chof_1178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.64 %
Parental protein coverage: 87.98 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEEAEPEEFVVEK-VLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGKEKDGTKR
EEAEPEEFVVEK.VLDRRV.NGKVEYFLKWKGF.DADNTWEPEENLD.PELIE.FLNSQKAGKEKDGT.R
RetrocopyEEAEPEEFVVEK>VLDRRVANGKVEYFLKWKGFADADNTWEPEENLDHPELIEEFLNSQKAGKEKDGTTR
ParentalKSLSDSESDDSKSKKK-RDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLA-KEANMK
KSLSDSES.D..SK.K.RDAADKPRGFARGLDPE..IGATDSSGELMFL.K..DSDEADL.L....AN.K
RetrocopyKSLSDSESED--SKSK>RDAADKPRGFARGLDPECMIGATDSSGELMFLKKRRDSDEADLGLS<RGANRK
ParentalCPQIVIAFYEERLTW-HSCPEDEAQ
CPQIV.AFYE.RLT..HSCP.DEAQ
RetrocopyCPQIVVAFYEARLTS<HSCPDDEAQ

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_1178 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 65 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000119572 retrocopies
Choloepus hoffmanni ENSCHOG00000013843 22 retrocopies
Cavia porcellus ENSCPOG000000151681 retrocopy
Felis catus ENSFCAG000000152246 retrocopies
Homo sapiens ENSG000001225659 retrocopies
Nomascus leucogenys ENSNLEG000000149319 retrocopies
Ochotona princeps ENSOPRG000000117139 retrocopies
Sorex araneus ENSSARG000000080112 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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