RetrogeneDB ID:

retro_chof_1504

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_310693:39..497(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COQ10B
Ensembl ID:ENSCHOG00000005807
Aliases:None
Description:coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]


Retrocopy-Parental alignment summary:






>retro_chof_1504
ATGGTTGCTTGGATTGGTCAGAGGGTCTTAAGGAAGGTGGTCTTGGGATGCTGTCCAAGTCCTGGGCAGGGGCCAGAGCC
TCAGCTCGGTTGCACCAACCTGCACGCAACGTCAGATATTTAGCTTTCCATGGTATATTGATAAGCAGAACTCTTCCATT
ACATACCTCAATTGTGCCTAAGGAGATATATGCAAGAACTTTCTTCAAAATTGCTGCACCGTTAATAAACAAAAGAAAAA
AATATTCAGAGAGGAGAAATGATAGGATATTCTATGTGGGAAATGTATGATGTGGTATCAGGAATGGAGGATTATAAGCA
TTTTGTTCCTTGGTGCAAAAAGTCAGATGTAATATCAAAGAGATCTGGACACTGCAAAACACGATTAGAAATTGGGTTTC
CAACCAAGTTGGAGCGATATACCTCAGAGTAACCTTGGTGGAACCACATTTGGTAAAG

ORF - retro_chof_1504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.28 %
Parental protein coverage: 65.68 %
Number of stop codons detected: 0
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMAARIGQRVLRKVVSGCCP-KSGAGAAAGASAPAHEGARNVRYLASCGILMNRTLPLHTSVVPKEIYART
M.A.IGQRVLRKVV.GCCP.KS.AGA.A..SA..H..ARNVRYLA..GIL..RTLPLHTS.VPKEIYART
RetrocopyMVAWIGQRVLRKVVLGCCP<KSWAGARA--SARLHQPARNVRYLAFHGILISRTLPLHTSIVPKEIYART
ParentalFFKIAAPLINKRKEYSERR-IIGYSMQEMYDVVSGMDDYKHFVPWCKKSDVISKRSGYCKTRLEIGFPPM
FFKIAAPLINKRK.YSERR..IGYSM.EMYDVVSGM.DYKHFVPWCKKSDVISKRSG.CKTRLEIGFP..
RetrocopyFFKIAAPLINKRKKYSERR>MIGYSMWEMYDVVSGMEDYKHFVPWCKKSDVISKRSGHCKTRLEIGFPTK
ParentalLERYTSV-VTLVKPHLVK
LERYTS..VTLV.PHLVK
RetrocopyLERYTSE<VTLVEPHLVK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST - click to see more details

Choloepus hoffmanni was not studied using EST data.

TSS - click to see more details

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab - click to see more details

retro_chof_1504 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 19 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000046592 retrocopies
retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni ENSCHOG00000005807 1 retrocopy
retro_chof_1504 ,
Callithrix jacchus ENSCJAG000000039711 retrocopy
retro_cjac_1836,
Dasypus novemcinctus ENSDNOG000000032292 retrocopies
retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii ENSDORG000000040901 retrocopy
retro_dord_508,
Erinaceus europaeus ENSEEUG000000016261 retrocopy
retro_eeur_401,
Felis catus ENSFCAG000000223851 retrocopy
retro_fcat_1487,
Homo sapiens ENSG000001155201 retrocopy
retro_hsap_3349,
Gorilla gorilla ENSGGOG000000233732 retrocopies
retro_ggor_2270, retro_ggor_569,
Myotis lucifugus ENSMLUG000000008651 retrocopy
retro_mluc_1236,
Macaca mulatta ENSMMUG000000104881 retrocopy
retro_mmul_2434,
Monodelphis domestica ENSMODG000000122811 retrocopy
retro_mdom_600,
Mus musculus ENSMUSG000000259811 retrocopy
retro_mmus_3224,
Nomascus leucogenys ENSNLEG000000068711 retrocopy
retro_nleu_1172,
Ochotona princeps ENSOPRG000000100913 retrocopies
retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii ENSPPYG000000130452 retrocopies
retro_pabe_2758, retro_pabe_576,
Pan troglodytes ENSPTRG000000127721 retrocopy
retro_ptro_2137,
Rattus norvegicus ENSRNOG000000144561 retrocopy
retro_rnor_1620,
Tarsius syrichta ENSTSYG000000126422 retrocopies
retro_tsyr_1213, retro_tsyr_1666,


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