RetrogeneDB ID:

retro_chof_2393

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_70995:5398..6122(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP1B3
Ensembl ID:ENSCHOG00000007515
Aliases:None
Description:ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:HGNC Symbol;Acc:806]


Retrocopy-Parental alignment summary:






>retro_chof_2393
TTGATCTTGCTCTTCTACCCAGTCTTCTATGAGCTCCTGGCTGCACTCTGCACGTTCACAGTGTGGGTCATGCTTCAGAC
TTTGAACGGCGAGCTTCCAAAATATCGTGACCAGATTCCTAGTTCAGGACTTACGGTTTTTCCAGAACCATTTACTGCAT
TGGAATATACAATCAGTTTGTCTGATTCAGGCTCCTATAAAGCATACATTGAAGACCTTACTAGTTTTCTAAAGCCATAT
GATTTAGAAGAACGGAGGAATCTCACAGTCTGTCCTGATGGAGTACTTTTTGAACAGAAGGGCCCAGATTATCAGGCATG
TCAGTTTCCTGTTCACTTACTTGAAGAATGCAGTGGTAGGAGAGATCCTGATTTTGGCTATTCCAGAGGAAAACCTTGTG
TTCTTGTGAAAATGAACAGAGTAATTGCATTAAAGCTTGAAGGAAAACCAAGGATAATGTGTGTTCCCAAGAATGGAAAC
ACTACAGTTTTATCAATTTATCCTTGCAATGGAATTGTAGACTTAAAATATTTTCCATATTATGGAAAAAATTGCATGTG
GGATATTTACAGCCAGTAGTTGCTGTCCAGCCAGTCTTTATCTTTAACAGCACCAAGAAAAAGTGACAGCTGAGTGCAAG
ATTGCTGGGGCACCCAACCTAAAAAGCCAGGATGATCGCAACAAGTTTTTGGGATGAGTTGTGTTCAAAATCACAGTGAA
TGCA

ORF - retro_chof_2393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.2 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalLILLFYLVFYGFLAALFTFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPFTALEYTISLSDSGSYKAYV
LILLFY.VFY..LAAL.TFT.WVMLQTLN.E.PKYRDQIPS.GL.VFP.PFTALEYTISLSDSGSYKAY.
RetrocopyLILLFYPVFYELLAALCTFTVWVMLQTLNGELPKYRDQIPSSGLTVFPEPFTALEYTISLSDSGSYKAYI
ParentalEDLTNFLKP-NVVEQKNLTVCPDGALFEQKGPDYHACQFPVHLLEECSGMRDPDFGYSKGKPCVLVKMNR
EDLT.FLKP....E..NLTVCPDG.LFEQKGPDY.ACQFPVHLLEECSG.RDPDFGYS.GKPCVLVKMNR
RetrocopyEDLTSFLKPYDLEERRNLTVCPDGVLFEQKGPDYQACQFPVHLLEECSGRRDPDFGYSRGKPCVLVKMNR
ParentalIIGLKPEGEPRIMCVPKDGNTAVLSTYPHNGIVDLKYFPYYG-KKLHVGYLQPVVAVQPVFSSNSTKK-E
.I.LK.EG.PRIMCVPK.GNT.VLS.YP.NGIVDLKYFPYYG.KKLHVGYLQPVVAVQPVF..NSTKK..
RetrocopyVIALKLEGKPRIMCVPKNGNTTVLSIYPCNGIVDLKYFPYYG<KKLHVGYLQPVVAVQPVFIFNSTKK<K
ParentalTTVECKIDGSPNLKSQDDRDKFLGRVVFKITVNA
.T.ECKI.G.PNLKSQDDR.KFLG.VVFKITVNA
RetrocopyVTAECKIAGAPNLKSQDDRNKFLG*VVFKITVNA

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_2393 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 36 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000141405 retrocopies
retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni ENSCHOG00000007515 4 retrocopies
retro_chof_1000, retro_chof_1421, retro_chof_2393 , retro_chof_2445,
Callithrix jacchus ENSCJAG000000019811 retrocopy
retro_cjac_309,
Cavia porcellus ENSCPOG000000037394 retrocopies
retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus ENSECAG000000198852 retrocopies
retro_ecab_1084, retro_ecab_468,
Homo sapiens ENSG000000698492 retrocopies
retro_hsap_1387, retro_hsap_2263,
Loxodonta africana ENSLAFG000000105531 retrocopy
retro_lafr_815,
Mus musculus ENSMUSG000000324122 retrocopies
retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys ENSNLEG000000046631 retrocopy
retro_nleu_1286,
Otolemur garnettii ENSOGAG000000086621 retrocopy
retro_ogar_2284,
Procavia capensis ENSPCAG000000139271 retrocopy
retro_pcap_350,
Pongo abelii ENSPPYG000000141691 retrocopy
retro_pabe_1953,
Pan troglodytes ENSPTRG000000154762 retrocopies
retro_ptro_1603, retro_ptro_951,
Rattus norvegicus ENSRNOG000000115012 retrocopies
retro_rnor_2571, retro_rnor_789,
Sus scrofa ENSSSCG000000116763 retrocopies
retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus ENSSTOG000000132351 retrocopy
retro_itri_1663,
Tupaia belangeri ENSTBEG000000010041 retrocopy
retro_tbel_3620,
Tarsius syrichta ENSTSYG000000002221 retrocopy
retro_tsyr_330,
Tursiops truncatus ENSTTRG000000120381 retrocopy
retro_ttru_333,


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