RetrogeneDB ID:

retro_chof_1003

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_18263:13922..14270(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POLR2D
Ensembl ID:ENSCHOG00000013850
Aliases:None
Description:polymerase (RNA) II (DNA directed) polypeptide D [Source:HGNC Symbol;Acc:9191]


Retrocopy-Parental alignment summary:






>retro_chof_1003
TTTGAAACAGCTGAGACACTTCTCGATTCAGAGTTCACATGCTTCTGGAGCATCAAAAGCAGCAGAACGAGAGTGCAGAG
GGTGAACAGGAACTCTCAGAGGTCTTCATGAAAACTTTGAACTATACGGTCCATTTCAATTGGTTCAAAAACAAAAAGAA
CATGCCTATGTCCATAAATTGTTGCTCCAGAAAAAAGCTTTATAAGTTCAAGTTGGCATGTCAGCACACCTTGCGCCCCA
GAGACTGCCAAGGAGTACAAGGCTCTGATTCCAAGCCTGGAAGGGCAGTTTGAAGATAAGGTGCTGCAACAGATTGTAGA
TGATACCCAGATAAAACATGGCTTTCAA

ORF - retro_chof_1003 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.67 %
Parental protein coverage: 99.15 %
Number of stop codons detected: 0
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalFETAETLLNSE-VHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETI-ASVRSLLLQ-KKL
FETAETLL.SE.VHMLLEH.KQQNESAE.EQELSEVFMKTLNYT..F..FKN.....A.V..LLLQ.KKL
RetrocopyFETAETLLDSE<VHMLLEHQKQQNESAEGEQELSEVFMKTLNYTVHFNWFKNKKNM<AYVHKLLLQ>KKL
ParentalHKFELACLANL-CPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQ
.KF.LAC...L..PETA.E.KALIPSLEG.FED..LQQI.DD.Q.K..FQ
RetrocopyYKFKLACQHTL>APETAKEYKALIPSLEGQFEDKVLQQIVDDTQIKHGFQ

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_1003 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 17 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000117461 retrocopy
retro_amel_1020,
Canis familiaris ENSCAFG000000043112 retrocopies
retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni ENSCHOG00000013850 3 retrocopies
retro_chof_1003 , retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus ENSDNOG000000085271 retrocopy
retro_dnov_734,
Felis catus ENSFCAG000000278161 retrocopy
retro_fcat_1148,
Gorilla gorilla ENSGGOG000000047231 retrocopy
retro_ggor_1658,
Macaca mulatta ENSMMUG000000019891 retrocopy
retro_mmul_1011,
Monodelphis domestica ENSMODG000000186534 retrocopies
retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furoENSMPUG000000166851 retrocopy
retro_mputfur_611,
Mus musculus ENSMUSG000000242581 retrocopy
retro_mmus_1331,
Oryctolagus cuniculus ENSOCUG000000214491 retrocopy
retro_ocun_35,
Ochotona princeps ENSOPRG000000053272 retrocopies
retro_opri_233, retro_opri_725,
Pongo abelii ENSPPYG000000127591 retrocopy
retro_pabe_1933,
Pan troglodytes ENSPTRG000000124361 retrocopy
retro_ptro_1571,
Sorex araneus ENSSARG000000090371 retrocopy
retro_sara_420,
Sarcophilus harrisii ENSSHAG000000148171 retrocopy
retro_shar_728,
Ictidomys tridecemlineatus ENSSTOG000000233293 retrocopies
retro_itri_1323, retro_itri_145, retro_itri_600,


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