RetrogeneDB ID:

retro_chof_72

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_1264:42777..43220(+)
Located in intron of:ENSCHOG00000003744
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DSTN
Ensembl ID:ENSCHOG00000003110
Aliases:None
Description:destrin (actin depolymerizing factor) [Source:HGNC Symbol;Acc:15750]


Retrocopy-Parental alignment summary:






>retro_chof_72
TCTGGAGTAACAGTGACTAATGAAGTCATCAAAGTTTTTAATAATATGAAAGTAAGGAAATCTACACAAGAGGAGATCAA
AAAAAGAAAAAAAGCAATTCTTTTCTGTTTAAGTGATGACAGAAGGCAAATAACTATAGTGGAAGTAAAGCAGATCTTGG
TGGGTGACGTTGGTGACACTGTAGAGGACCCCTACACATCTTTTTGTGAAGTTGCTACATCTGAATGACTGCTGATATGC
TTTGTACAGTGCCAAATATGAAACAAAAGAGTCTTAAGAAAGAAGACCTAGTATTTATATTCTGGGCTCCTCAAAGTGTA
CCTTTAAAAAGCAAGATGATTTATGCTAGTAAAGATGCCATTAAAAAGAAATTTACAGGTATTAAACATGAGTGGCAAGT
AAATGGCTTGGATGATATTAAGGACTGCTCAACACTGGAGAGA

ORF - retro_chof_72 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.63 %
Parental protein coverage: 91.41 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalASVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIFCLSADKKCIIVEEGKEILVGDVGVTITDPFKH-F
..V.V..EV...F..MKVRK.ST.EEI.....A..FCLS.D...I...E.K.ILVGDVG.T..DP....F
RetrocopySGVTVTNEVIKVFNNMKVRK-STQEEIXXXXXAILFCLSDDRRQITIVEVKQILVGDVGDTVEDPYTS>F
ParentalVGMLPEKDCRYALYDASFETKES-RKEELMFFLWAPELAPLKSKMIYASSKDAIKKKFQGIKHECQANGP
V..L...DC.YALY.A..ETKES..KE.L.F..WAP...PLKSKMIYA.SKDAIKKKF.GIKHE.Q.NG.
RetrocopyVKLLHLNDC*YALYSAKYETKES>KKEDLVFIFWAPQSVPLKSKMIYA-SKDAIKKKFTGIKHEWQVNGL
ParentalEDLNRACIAEK
.D.......E.
RetrocopyDDIKDCSTLER

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_72 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 20 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000154341 retrocopy
retro_btau_880,
Choloepus hoffmanni ENSCHOG00000003110 5 retrocopies
retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72 ,
Cavia porcellus ENSCPOG000000055732 retrocopies
retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus ENSDNOG000000009341 retrocopy
retro_dnov_24,
Erinaceus europaeus ENSEEUG000000118931 retrocopy
retro_eeur_529,
Homo sapiens ENSG000001258681 retrocopy
retro_hsap_952,
Gorilla gorilla ENSGGOG000000090071 retrocopy
retro_ggor_768,
Microcebus murinus ENSMICG000000136871 retrocopy
retro_mmur_765,
Macaca mulatta ENSMMUG000000137861 retrocopy
retro_mmul_782,
Mus musculus ENSMUSG000000159321 retrocopy
retro_mmus_3314,
Nomascus leucogenys ENSNLEG000000096791 retrocopy
retro_nleu_2458,
Oryctolagus cuniculus ENSOCUG000000274561 retrocopy
retro_ocun_1891,
Ochotona princeps ENSOPRG000000009762 retrocopies
retro_opri_1078, retro_opri_696,
Pongo abelii ENSPPYG000000107271 retrocopy
retro_pabe_812,
Pan troglodytes ENSPTRG000000132751 retrocopy
retro_ptro_659,
Pteropus vampyrus ENSPVAG000000004201 retrocopy
retro_pvam_1275,
Rattus norvegicus ENSRNOG000000059241 retrocopy
retro_rnor_1710,
Sus scrofa ENSSSCG000000070851 retrocopy
retro_sscr_954,
Tupaia belangeri ENSTBEG000000176348 retrocopies
retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus ENSTTRG000000072911 retrocopy
retro_ttru_1503,


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