RetrogeneDB ID:

retro_chof_2387

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_70713:5340..5878(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMD14
Ensembl ID:ENSCHOG00000002556
Aliases:None
Description:proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]


Retrocopy-Parental alignment summary:






>retro_chof_2387
CAGTCAGGAACAGGTGTCAGTGTGGAGGCAGTTGATCCAGTATTCCAAATCAAAATGTTGGATATTTTGAATCAGACAGG
AAGGCCTGAGATGATTATTGGTTGGTATCACAGTCACCCTGGCTTTCGCTTGTTGACTTTCTGGTGTGGATATCAACACT
CAACGGAGCTTTGAAGCCTTGTCAGAGAGAGCCATGGCAGTGGTTGTGGATCCCATTCAGAGTGCAAAAGGAAAGGTTGT
TATTGATGCCTTCAGATTGATCAATGCTAATATGATGGTCTTAGGACATAAACCAAGACAAACAACTTCAAATCTGGATC
ACTTAAACAAGCCATCTATCCAGGCATTAATTAATGGACTAAACAGACATTATTACTCCATTACTATTAACTATTGGAAA
AATGAACTGGAACAGAAGATGTTGTTAAATTTGTATAAGAAGAGTTGGATGGAAGGTTTAACACTTCAGGACTACAGAGA
ACACTATATACATAATGAATCAGTGGTAAAAGAAATGTTGGCATTAGTCAAGAATTAC

ORF - retro_chof_2387 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.33 %
Parental protein coverage: 60.27 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGF-GCWLSGVDINTQQSFEALSERAVAVVV
QSGTGVSVEAVDPVFQ.KMLD.L.QTGRPEM..GWYHSHPGF..C.LSGVDINTQ.SFEALSERA.AVVV
RetrocopyQSGTGVSVEAVDPVFQIKMLDILNQTGRPEMIIGWYHSHPGF>AC*LSGVDINTQRSFEALSERAMAVVV
ParentalDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKNELEQK
DPIQS.KGKVVIDAFRLINANMMVLGH.PRQTTSNL.HLNKPSIQALI.GLNRHYYSITINY.KNELEQK
RetrocopyDPIQSAKGKVVIDAFRLINANMMVLGHKPRQTTSNLDHLNKPSIQALINGLNRHYYSITINYWKNELEQK
ParentalMLLNLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNY
MLLNL.KKSWMEGLTLQDY.EH..HNESVVKEML.L.KNY
RetrocopyMLLNLYKKSWMEGLTLQDYREHYIHNESVVKEMLALVKNY

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_2387 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 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000002556 1 retrocopy
retro_chof_2387 ,
Callithrix jacchus ENSCJAG000000055721 retrocopy
Gorilla gorilla ENSGGOG000000157471 retrocopy
Mus musculus ENSMUSG000000269141 retrocopy
Otolemur garnettii ENSOGAG000000049332 retrocopies
Pongo abelii ENSPPYG000000128811 retrocopy
Pan troglodytes ENSPTRG000000125751 retrocopy
Rattus norvegicus ENSRNOG000000049111 retrocopy
Tupaia belangeri ENSTBEG000000141181 retrocopy



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