RetrogeneDB ID:

retro_chof_236

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:GeneScaffold_5151:51715..52209(-)
Located in intron of:ENSCHOG00000010823
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MKI67IP
Ensembl ID:ENSCHOG00000002227
Aliases:None
Description:MKI67 (FHA domain) interacting nucleolar phosphoprotein [Source:HGNC Symbol;Acc:17838]


Retrocopy-Parental alignment summary:






>retro_chof_236
ACAACGAAAAACTACCTTTTTGGTGAAAGGCTCTTGAAGTGTGAGTTTATGGCACCTGAAAAAGTACATGAACTTTACAA
AGACTGGGATGTTCCGTTTGCAAAGCCATCACATCCAGCAGTGAAACAGTATAATAAGAAACAGACACTTACAGAAAAGC
TACAGGTGGAGAAGTGATTTAAAAATGAAAAATTACTCAGGAAGAAATTAGCTCAAAAAGGAATAAAATACGATTTTCCT
TCATTGATACTTAGGAAAGAAAAAAAGAAATTGTTTTTTTCAGAAGTCTATGAATGGCCAGGTTTTCCAGAACAAGAGGT
TTCAGGAACTCCTAACATTCCTAAGAGCACTGGAGATAGCCAGGGCCCCACACCAGTTTGCACACCATTTTTGGAAAAGG
AAAAATCTGAAGTGGCTGAAATGAATGATAATGAAATAGTTTTCAACAGCCCATATATGGCACAAAAGAAGAAACACAAG
AGACTCAAACACCT

ORF - retro_chof_236 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.98 %
Parental protein coverage: 69.11 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTMNNYLFGERLLKCEFLESEKVHKELFKDWDVPFAKPSHPAVKRYNKKRTLIEKLRMEKRFKNKEKLLRK
T..NYLFGERLLKCEF...EKVH.EL.KDWDVPFAKPSHPAVK.YNKK.TL.EKL..EK.FKN.EKLLRK
RetrocopyTTKNYLFGERLLKCEFMAPEKVH-ELYKDWDVPFAKPSHPAVKQYNKKQTLTEKLQVEK*FKN-EKLLRK
ParentalKLAQKGIKYDFPSLI-LRKEKKRNASNTVLQKSTNSQV-FPNKKKQKVSGNPTTPKSTGDSQGPTPVCTP
KLAQKGIKYDFPSLI.L.K.K.....N...QKS.N.QV.FP....Q.VSG.P..PKSTGDSQGPTPVCTP
RetrocopyKLAQKGIKYDFPSLI>LGKKKR----NCFFQKSMNGQV<FP---EQEVSGTPNIPKSTGDSQGPTPVCTP
ParentalTFLERRKSEVTEMNDNDEDNEIVF-KEPISGAKEEKQETQTP
.FLE..KSEV.EMNDN.....IVF...PI.G.KEE.QETQTP
Retrocopy-FLEKEKSEVAEMNDNE----IVF<QQPIYGTKEETQETQTP

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_236 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 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000193871 retrocopy
retro_btau_1516,
Choloepus hoffmanni ENSCHOG00000002227 5 retrocopies
retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236 , retro_chof_2480,
Callithrix jacchus ENSCJAG000000133861 retrocopy
retro_cjac_3076,
Dasypus novemcinctus ENSDNOG000000050172 retrocopies
retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus ENSEEUG000000085353 retrocopies
retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens ENSG000001554385 retrocopies
retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553,
Gorilla gorilla ENSGGOG000000234984 retrocopies
retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana ENSLAFG000000307311 retrocopy
retro_lafr_500,
Microcebus murinus ENSMICG000000157871 retrocopy
retro_mmur_990,
Myotis lucifugus ENSMLUG000000064812 retrocopies
retro_mluc_1217, retro_mluc_1369,
Macaca mulatta ENSMMUG0000002092811 retrocopies
retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica ENSMODG000000001522 retrocopies
retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys ENSNLEG000000011634 retrocopies
retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii ENSPPYG000000258752 retrocopies
retro_pabe_2248, retro_pabe_510,
Pan troglodytes ENSPTRG000000124195 retrocopies
retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus ENSPVAG000000167071 retrocopy
retro_pvam_134,
Sorex araneus ENSSARG000000062521 retrocopy
retro_sara_362,
Tupaia belangeri ENSTBEG000000011234 retrocopies
retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos ENSVPAG000000058472 retrocopies
retro_vpac_136, retro_vpac_265,


Copyright © RetrogeneDB 2014-2017