RetrogeneDB ID:

retro_dnov_1801

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_311:77277..78352(+)
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:ENSDNOG00000017353
Aliases:None
Description:core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]


Retrocopy-Parental alignment summary:






>retro_dnov_1801
ATGGCCTCTAAATCTAGGCTGAATTTTTTATCTTCCTCTGTGGCTCAGCAATCAGATTTTTTAATATGTTCTCTGCTATT
TAATATTTTGTAAAAGAAAAAGTGATACCCAGCCTAATATTCTTCACAATGATCCTCATGCTAGACATTCAGATGATAAT
GGACAGAGTCACCTGGAAGGACTGGTGAACTTCATTGCAGATGCCAACCAACATAAAGATGAGGACACAGACATGACTGA
GAAACTCTATCAGAAGGTTAAAATTCTTTGTTGGGTTATGTCAAGACCTCAAATTCTAGAAAAAAGGCCAAACACATCAA
AGTTACATGACCCCAGTGTTACGAAGTTTTGTTTATGAGCTCAGAAGAAAATTAAGACTTCCCTACTGTGGGATTAAGAA
CCAAAGGCAGAGATCAACTATACTGGAAAACAATTAAAGCTTTCAGTTTGTTTATGACTATTATTTAAAAGATCCTGATT
GGTTCTGAAAGCAGATGATGATACATATGTCAAACTAGACAATTTAAGATGACTTATTTCAAAATTTGATCCTGAAAAAC
CCATTTACTTTGGGAGAAGATTTAAGCCTGATGTAAAGCAGGGCTGCATGAGTGGAGGAGAGGGATATATATTGAACAAG
GAAGACTTGCAGAGATTCGTTGATGCATTTAAAATGGACAAATGACACATTCGTTCCTCCACTGAAAACTCAGCACTGGG
GAGATGCATGGAAATTATAAATGTGGAGGCGAGAGATTCCAGAGTTACGACTGGAAAGGAAACTGTTCATCTCTTTGTAC
CCAAACACCACTTAATCAAAGGTTATCTACCCAAAACGTTTTGGTACTTCAATTATAACTAGTATTCTCCAGTAGAGGGT
CCCAGATGCTGTTCTGATCTTGCAATTTCTACTCATTATGTTGATCCTTTAACTAATTATGAGTTAGAATACTTTGTTTA
TCATCTTCTCCCATATGGTTATTTGTACAGATATCAACCTGCTTTACCTGAGAACATACTAATAGAAATAATTGAAACAT
ACAAAAATGATGATCCAAAGGTAAAATTAGAAAAC

ORF - retro_dnov_1801 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.46 %
Parental protein coverage: 99.72 %
Number of stop codons detected: 5
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMASKSWLNVL-IFLCGSAVGFF-LCSQLFSTLL-EEQSDTQPNILHNDPHARHSDDNGQHHLEGQMNFNA
MASKS.LN.L.IFLCGSA..FF..CS.L....L....SDTQPNILHNDPHARHSDDNGQ.HLEG..NF.A
RetrocopyMASKSRLNFL<IFLCGSAIRFF>ICS-LLFNIL>KRKSDTQPNILHNDPHARHSDDNGQSHLEGLVNFIA
ParentalDVNQHKDEDTDIAEKLYQKVKILCWVMTGPQNLEK-KAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKT
D.NQHKDEDTD..EKLYQKVKILCWVM..PQ.LEK.KAKH.K.T..Q.C..VLFMSSEEN.DFPTVGL.T
RetrocopyDANQHKDEDTDMTEKLYQKVKILCWVMSRPQILEK<KAKHIKVT*PQ-CYEVLFMSSEEN*DFPTVGLRT
ParentalKEGRDQLYWKTIKAF-QYVYDHYLEDADWF-MKADDDTYVILDNLRWLLSKYDPQNPIYFGRRFKPFVKQ
K.GRDQLYWKTIKAF.Q.VYD.YL.D.DWF..KADDDTYV.LDNLR.L.SK.DP..PIYFGRRFKP.VKQ
RetrocopyK-GRDQLYWKTIKAF<QFVYDYYLKDPDWF<LKADDDTYVKLDNLR*LISKFDPEKPIYFGRRFKPDVKQ
ParentalGYMSGGAGYVLSKEALKRFVDAFKTEKCTHSSSIEDLALGRCMEIMNVEAGDSRDTTGKETFHPFVPEHH
G.MSGG.GY.L.KE.L.RFVDAFK..K....SS.E..ALGRCMEI.NVEA.DSR.TTGKET.H.FVP.HH
RetrocopyGCMSGGEGYILNKEDLQRFVDAFKMDK*HIRSSTENSALGRCMEIINVEARDSRVTTGKETVHLFVPKHH
ParentalLIKGYLPKTFWYWNYNYYPTVEGPGCCSDLAISFHYVDPLTMYELEYLVYHLRPY-YLYRY-PALPEN--
LIKGYLPKTFWY.NYN.Y..VEGP.CCSDLAIS.HYVDPLT.YELEY.VYHL.PY.YLYRY.PALPEN..
RetrocopyLIKGYLPKTFWYFNYN*YSPVEGPRCCSDLAISTHYVDPLTNYELEYFVYHLLPYGYLYRYQPALPENIL
ParentalVKEIGENTNDDPKVKKKN
...I....NDDPKVK..N
RetrocopyIEIIETYKNDDPKVKLEN

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 0 .00 RPM 109 .10 RPM
SRP012922_cerebellum 0 .00 RPM 1 .37 RPM
SRP012922_heart 0 .00 RPM 2 .09 RPM
SRP012922_kidney 0 .00 RPM 18 .07 RPM
SRP012922_liver 0 .00 RPM 5 .73 RPM
SRP012922_lung 0 .00 RPM 3 .51 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .38 RPM
SRP012922_spleen 0 .00 RPM 9 .27 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_1801 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 ENSCHOG000000002252 retrocopies
Dasypus novemcinctus ENSDNOG00000017353 2 retrocopies
retro_dnov_1801 , retro_dnov_1905,
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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