RetrogeneDB ID:

retro_dnov_1184

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_15940:87262..88472(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSDNOG00000019151
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_dnov_1184
GTGTCCTTCTTGGTCAGACTGCTTGTACTCCCATTCAGCTTGAGCCTGATTTGGCACTCACAAACATTGCTTCTGGGACA
TCAGAACAGACCAAGGCTGTGGTAGATGGAGGTACTATCTCAGCATTCATTTCTCTGTTGGCATCTCTGCATGTTCACTT
ATGGGAACAAGCTCTTTGGACTTTAGGAAACATTGCAGGTGATGGCTCATCTTTCCAAGACTTGGTTATCAAGTCTGGTG
AAATTGATCCTCTGTTGGATCTACTTGCAGTTCCTGAAATATCATCTTAATCACATAGTTACTTATGTAAACTTTCCTGG
ACATTTTCAAACCTTTGTTGAAGCAAGAATCCTGAACCCCTGTTAGATGCTGTTGAGCAAATTTTTCCTACTCTAGTTCA
TCTGCATCCTGATGACCTGTAAGTATTAGTAGATACCTGCTGGGCCACTTCCTATCTTACTGATGGTCCAAAGAAATGCA
TTGAAATGCTTGAGAAAATTGGAGTTGTGCCCCAGCTTGTGAAGCTCCTAGGTGCTCTGAATTGCCAAGTATGACTCCCG
CACTAAGTACCAAAGGGAATAATGTTACTGGGACAGATGAACAGACTCAGGTTGTAATAGATGAAGGAGCACTTACTGTC
TTTCCCAACCTGCTAATTAACTCAAAAACTAATATTCAGAAAGCAGCTTCCTGGACAATGTCAAACATCACAGTTGGCCA
TCAGTACCAGATACAGCAAGTAGTGAATCATGGATTGGTCCCTTTCCTCATTAGCGTTCTTTCTAAGGAAGACTTTAAGA
CACAAAAGGAAGCTGTATGGGCTGTGACCAACTATACAAGTGGTGGAACAGTTGAACAGATTGTATACCTTGTCCATTGT
GGCATAATAGAACCTTTGATGAACCTTTTAACTGCAAAGGATACCAAAATTATTCTGGTTATTCTGGATGCCATTTCAAA
TATCTTTCAGGCTGCTGAGAAACTAGGTGAAACTGAGAAACTTAGTATAATGATTGGAGAATGTCAAGGATTGGACAAAA
TTGAAGGTCTACAAAACCATGAAAATGAGTTTGTTTTCAAGGCTTAATTAAGCTTTGTTGAGAAGTATTTCTCTGTAAAG
AAAGAAGATGATCAGAACGTTGTACCAGAAACTACCTCTGAAGTTTATTCTTTCCAAGTTCAGGATGGTACTCTTGGGAC
TTTTAACTTT

ORF - retro_dnov_1184 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.62 %
Parental protein coverage: 99.75 %
Number of stop codons detected: 4
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalVSFLDR-TDCTPIQFESAWALTNIASGTSEQTKAVVDGGGIPAFVSLLASPHAHISEQAVWALGNIAGDG
VSFL.R.T.CTPIQ.E...ALTNIASGTSEQTKAVVDGG.I.AF.SLLAS.H.H..EQA.W.LGNIAGDG
RetrocopyVSFLVR<TACTPIQLEPDLALTNIASGTSEQTKAVVDGGTISAFISLLASLHVHLWEQALWTLGNIAGDG
ParentalSAFRDLVIKYGAIDPLLALLAPPNMSSLAYSYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLIRLLHHD
S.F.DLVIK.G.IDPLL.LLA.P..SS...SYL..L.WT.SNLC..KNP.P.LDAVEQI.PTL..L.H.D
RetrocopySSFQDLVIKSGEIDPLLDLLAVPEISS*SHSYLCKLSWTFSNLC*SKNPEPLLDAVEQIFPTLVHL-HPD
ParentalDPEVLTDTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGA-TQLPIVTPALRAIGNIVTGTDEQTQVVI
D..VL.DTCWA.SYLTDGP...IEM..K.GVVPQLVKLLGA...LP..TPAL...GN.VTGTDEQTQVVI
RetrocopyDL*VLVDTCWATSYLTDGPKKCIEMLEKIGVVPQLVKLLGA<SELPSMTPALSTKGNNVTGTDEQTQVVI
ParentalDAGALAVFPSLLTNSKNNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSQAEFKTQKEAVWAVT
D.GAL.VFP.LL.NSK.NIQK.A.WTMSNIT.G.Q.QIQQVVNHGLVPFL.SVLS...FKTQKEAVWAVT
RetrocopyDEGALTVFPNLLINSKTNIQKAASWTMSNITVGHQYQIQQVVNHGLVPFLISVLSKEDFKTQKEAVWAVT
ParentalNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDK
NYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMI.EC.GLDK
RetrocopyNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIGECQGLDK
ParentalIEALQNHENESVYKASLSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGTPGTFNF
IE.LQNHENE.V.KA.LS..EKYFSV..E.DQNVVPETTSE.Y.FQVQDGT.GTFNF
RetrocopyIEGLQNHENEFVFKA*LSFVEKYFSVKKEDDQNVVPETTSEVYSFQVQDGTLGTFNF

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






RNA-Seq - click to see more details

(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 30 .34 RPM
SRP012922_cerebellum 0 .00 RPM 8 .94 RPM
SRP012922_heart 0 .00 RPM 8 .82 RPM
SRP012922_kidney 0 .00 RPM 6 .30 RPM
SRP012922_liver 0 .00 RPM 4 .02 RPM
SRP012922_lung 0 .00 RPM 9 .77 RPM
SRP012922_quadricep_muscle 0 .00 RPM 14 .71 RPM
SRP012922_spleen 0 .00 RPM 33 .99 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_1184 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 23 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG00000019151 6 retrocopies
retro_dnov_1184 , retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


Copyright © RetrogeneDB 2014-2017