RetrogeneDB ID:

retro_chof_1398

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_28286:5948..6472(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP9
Ensembl ID:ENSCHOG00000013286
Aliases:None
Description:retinoblastoma binding protein 9 [Source:HGNC Symbol;Acc:9892]


Retrocopy-Parental alignment summary:






>retro_chof_1398
ATTCCTGGGAATGGAGGCAGGGATGTGGCCACGCACAGCTGGTACGGCTGGGTGAGAATGGGGCTGGAGCAGATACCTGG
TTTCCAGTGTTTGGCTAAAAACATGCCTGACCCAATTTGGCTCAAGAGAGCATCTGGCTGCCCTTCTTGGAGACGGAGCT
CCACTGTGATGACAAGACCATCATCATAGGCTACGGTTCCAGGGCCACTGATGCCATGAGGTATGCAGAGACACATTGAG
TCTATGCTGTTATATTAGTGGCTGCCTACACATCAGACCCAGGGGATGAAAATGAGCGGGCAAGTGGATACTTCTACCGT
CCCTGGCAGTGGGAGAAGATCAAGGCCAACTGCCCTCACATTGTACAGTTTGGGTCTACAGATGATCCTTTCCTTCCCTG
GAAAGAGCAACAAGAAGTTGCTGATAGGCTGGAAGCCAAATTGTACAAATTCACTGATCGTGGCCACTTTCAGGTCACTG
AGTTTCACGAACTGATTAGCGTAGTGAAGTCTACGCTGAAAATA

ORF - retro_chof_1398 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.55 %
Parental protein coverage: 94.09 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVPGNGGGDVATHGWYGWVRKGLEQIPGFQCLAKNMPDPF-MARESIWLPFMETELHCDDKTIIIGHSSGA
.PGNGG.DVATH.WYGWVR.GLEQIPGFQCLAKNMPDP...A.ESIWLPF.ETELHCDDKTIIIG..S.A
RetrocopyIPGNGGRDVATHSWYGWVRMGLEQIPGFQCLAKNMPDPI<LAQESIWLPFLETELHCDDKTIIIGYGSRA
ParentalIAAMXXXXXXXXXXXXXXXAYTSDLGNENERASGYFNRPWQWEKIKANCSHIVQFGSTDDPFLPWKEQQE
..AM...............AYTSD.G.ENERASGYF.RPWQWEKIKANC.HIVQFGSTDDPFLPWKEQQE
RetrocopyTDAMRYAETH*VYAVILVAAYTSDPGDENERASGYFYRPWQWEKIKANCPHIVQFGSTDDPFLPWKEQQE
ParentalVADRLEAKLYKFTDRGHFQNTEFHELISVVKSMLKV
VADRLEAKLYKFTDRGHFQ.TEFHELISVVKS.LK.
RetrocopyVADRLEAKLYKFTDRGHFQVTEFHELISVVKSTLKI

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_1398 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 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000013286 1 retrocopy
retro_chof_1398 ,
Callithrix jacchus ENSCJAG000000051701 retrocopy
Macaca mulatta ENSMMUG000000041461 retrocopy
Rattus norvegicus ENSRNOG000000079721 retrocopy



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