RetrogeneDB ID:

retro_chof_1782

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_382587:25..1096(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C1GALT1
Ensembl ID:ENSCHOG00000000225
Aliases:None
Description:core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]


Retrocopy-Parental alignment summary:






>retro_chof_1782
TGGCTGAATTTTTTAATCTTCCTCCATGGATCAGCAATCGGATTTTTTTTTTTTTAATGTTCTCAGCTATTTAGTATTTT
GTTGGAAGAACGAGTGATACCCAAGCTAATACTTTTCATAATGATCCTCATGCTAGACATGCAGATGGTAACAGACAGAA
TCATCTAGAAGGACAAATGAACTTCAGTGCTGATGTTAGCCAACATAAAGATGACGACACAGACCTCGCTGAAAAACTCT
ACCAGAAGATTAAAATTCTTTGCTGGGTTATGACAGGACCTCAAAATTCAGAGAAAAAGGCCAAACATGTCAAAGCTACA
TGGACCCAATGTTGTAATGAAGTTCTGTTTATGAGTTCAGAAGAAAATAAAGACTTCCCTACTGTGGGATTAAAAACCAA
AGGCAGAGAGCAACTATACTGGAAAACAATTAAAGCTTTTCAGTATGTTTATGACCATTATTTAGAAGATGGTGATTGGT
TACGAAAGCAGATGATGATACACATTTCATACGAGACAACTTGAGATGCCTTCTTTCAAAATATGACCCTGAAAAACCCA
TTTACTTTGGGAGAAGATTTAAGCCCTACGTAAAGCAGGCCTACATGAGTGGAGGAGCAGGCTGTGTATTGAGCAAGGAA
GCCCTGAAGAGATTTGTTGATGCATTTAAAGCAAAGAAATGTACACACAGTTCCTCCATCAAAGATTTAGCACTGGAAGA
TGCATGGAAATTACAGATGTAGAAGCAGGAGATTCCAGAGATACCACTGGGAAAGAAACCTTTCATCCCTGTGTACCAGA
ACACCACTTAATCAAAGGTTATCTATCCAAAACATTTTGGTACTGGGATTATAACTATCATTCTCCTGTAGAGGGTCCTG
GATGCTATTCTGACCTCGCAATTTCTTTTCATTATATTGACCCGCTACCTACGTATGAGTTAGAATACCTCATTTATCAT
CTTCACCCATATGGTTATTTACACAGATATCAACCTGCCTTACCTGAGAATATACTAAAGAAAATAAGTGAAACACACAA
ATATGATGATCCAAAAGTAAAATTAGGAAAC

ORF - retro_chof_1782 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.04 %
Parental protein coverage: 98.34 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalWLNFLIFLCGSAIGFFL--CSQLFSILLEEQ-SDTQPNILHNDPHARHSDDNGQNHLEGQMNFNADTSQH
WLNFLIFL.GSAIG.....CSQLFSILLEE..SDTQ.N..HNDPHARH.D.N.QNHLEGQMNF.AD.SQH
RetrocopyWLNFLIFLHGSAIGXXXXXCSQLFSILLEER<SDTQANTFHNDPHARHADGNRQNHLEGQMNFSADVSQH
ParentalKDEDTDIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKTKEGRDQ
KD.DTD.AEKLYQK.KILCWVMTGPQN.EKKAKHVKATW.Q.CN.VLFMSSEENKDFPTVGLKTK.GR.Q
RetrocopyKDDDTDLAEKLYQKIKILCWVMTGPQNSEKKAKHVKATWTQCCNEVLFMSSEENKDFPTVGLKTK-GREQ
ParentalLYWKTIKAFHYVYDHHLEDADWFMK-ADDDTYVILDNLRWLLSKYDPEKPIYFGRRFKPFVKQGYMSGGA
LYWKTIKAF.YVYDH.LED.DW..K.ADDDT..I.DNLR.LLSKYDPEKPIYFGRRFKP.VKQ.YMSGGA
RetrocopyLYWKTIKAFQYVYDHYLEDGDWLRK<ADDDTHFIRDNLRCLLSKYDPEKPIYFGRRFKPYVKQAYMSGGA
ParentalGYVLSKEALKRFVDAFRTDKCTHSSSIEDLAL-GRCMEIMNVEAGDSRDTTGKETFHPFVPEHHLIKGYL
G.VLSKEALKRFVDAF...KCTHSSSI.DLAL.GRCMEI..VEAGDSRDTTGKETFHP.VPEHHLIKGYL
RetrocopyGCVLSKEALKRFVDAFKAKKCTHSSSIKDLAL<GRCMEITDVEAGDSRDTTGKETFHPCVPEHHLIKGYL
ParentalPKTFWYWNYNYYPPVEGPGCCSDLAISFHYVDPLTMYELEYLVYHLRPYGYLYRYQPALSENRLREITE-
.KTFWYW.YNY..PVEGPGC.SDLAISFHY.DPL..YELEYL.YHL.PYGYL.RYQPAL.EN.L..I.E.
RetrocopySKTFWYWDYNYHSPVEGPGCYSDLAISFHYIDPLPTYELEYLIYHLHPYGYLHRYQPALPENILKKISET
Parental-KNDDPKVKLGN
.K.DDPKVKLGN
RetrocopyHKYDDPKVKLGN

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_1782 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 10 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000000225 2 retrocopies
retro_chof_1782 , retro_chof_2581,
Dasypus novemcinctus ENSDNOG000000173532 retrocopies
Homo sapiens ENSG000001063922 retrocopies
Loxodonta africana ENSLAFG000000000631 retrocopy
Myotis lucifugus ENSMLUG000000147891 retrocopy
Macaca mulatta ENSMMUG000000163381 retrocopy
Oryctolagus cuniculus ENSOCUG000000260021 retrocopy
Otolemur garnettii ENSOGAG000000128471 retrocopy
Petromyzon marinus ENSPMAG000000015621 retrocopy
Pan troglodytes ENSPTRG000000189252 retrocopies



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