RetrogeneDB ID:

retro_chof_1129

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_207053:1110..1648(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DCUN1D1
Ensembl ID:ENSCHOG00000013358
Aliases:None
Description:DCN1, defective in cullin neddylation 1, domain containing 1 [Source:HGNC Symbol;Acc:18184]


Retrocopy-Parental alignment summary:






>retro_chof_1129
AGCAAGCTGAAATCATCGCAGAAGGATAAAGTTTGTCAGTTACGATCTTCACGCAATCTAGGGAAAAAACAGCAATAAGT
TGTCTGTCTCAAAACGAAATTAGAGGTTGCAACAGGCAATTATTTCCAAAATCCTGAACTTTATATATGAGAGAGTGTAA
AAGGATCATTGGACAGGAAGAACTTAGAACAACTGTACAATAGATACAAAGGTCCTCAAGATGAAAACAAAATTGGAATA
GACGGTATACAGTAGTTCTGTGTGACCTGGCACTCGATCCAGCCAGCATTAGTGTGTTGATCACTGAGTGGAATTCTGGA
GCAGCAACACAGTGTGAGTTCTCCAAAATGGAGTCCATGGATGGTATGACAGAATTAGGGTGTGACAGCACAGAAAAACT
AAAGGCCCAGATACCAAGATGGAACAAGAACTGAAAGAACCAAGACGATTTAAGGATTTTTACCAGTTTACTTTTAATTT
TGCAAAGAATCCAGGACAAAAAGGATTAGATCTAGAAACGGCCATTGACTACAGAATT

ORF - retro_chof_1129 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.68 %
Parental protein coverage: 71.37 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNKLKSSQKDKVRQFMIFTQSSEKTA-VSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
.KLKSSQKDKV.Q.........K...V.CL.....KL.VAT.N.FQNPELYI.ESVKGSLDRK.LEQLYN
RetrocopySKLKSSQKDKVCQLRSSRNLGKKQQ*VVCLKT---KLEVATGNYFQNPELYI*ESVKGSLDRKNLEQLYN
ParentalRYKDPQDENKIGIDGIQQFC-DDLALDPASIIVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKA
RYK.PQDENKIGIDGIQ.FC..DLALDPASI.VLI..W...AATQCEFSK.E.MDGMTELGCDS.EKLKA
RetrocopyRYKGPQDENKIGIDGIQ*FC<CDLALDPASISVLITEWNSGAATQCEFSKMESMDGMTELGCDSTEKLKA
ParentalQIP-KMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIYWNL
QIP.KMEQELKEP.RFKDFYQFTFNFAKNPGQKGLDLE.AI....
RetrocopyQIP<KMEQELKEPRRFKDFYQFTFNFAKNPGQKGLDLETAIDYRI

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_1129 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 15 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000078214 retrocopies
Choloepus hoffmanni ENSCHOG00000013358 14 retrocopies
Callithrix jacchus ENSCJAG000000051482 retrocopies
Cavia porcellus ENSCPOG000000220864 retrocopies
Dasypus novemcinctus ENSDNOG000000190732 retrocopies
Echinops telfairi ENSETEG000000001661 retrocopy
Homo sapiens ENSG000000430931 retrocopy
Gorilla gorilla ENSGGOG000000107671 retrocopy
Macaca mulatta ENSMMUG000000105521 retrocopy
Mustela putorius furoENSMPUG000000023691 retrocopy
Mus musculus ENSMUSG000000277081 retrocopy
Nomascus leucogenys ENSNLEG000000059831 retrocopy
Otolemur garnettii ENSOGAG000000006581 retrocopy
Pan troglodytes ENSPTRG000000156611 retrocopy
Tarsius syrichta ENSTSYG000000122761 retrocopy



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