RetrogeneDB ID:

retro_dnov_417

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_452:190973..191279(+)
Located in intron of:ENSDNOG00000014522
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPT1
Ensembl ID:ENSDNOG00000000653
Aliases:None
Description:tumor protein, translationally-controlled 1 [Source:HGNC Symbol;Acc:12022]


Retrocopy-Parental alignment summary:






>retro_dnov_417
CTCACTGGTGGGACGGCCTCCGCCAAGGCCCTAGGCTGAAGGCATCGCAGGCACAGCCCCTGCTGGTGCTGACATTGTCA
TAAACCATCACTCTCAGGAAACCCGCTTCACAAAAGAAGCCTACAAGAAGTACTTAAAAGATGATGAAATCCATCAAAGG
CCAACTGAAGACCAGAGCTCAGAAAGGGTAACTCTTTTATGACAGGGGCCGCAGAACAAATCCACATCCTTGCCATATTC
AACAACCATCTGTTCTTTATTGGTGAAAACATGAGCCCAGATGGTGTGGTGGTGGCTCTTCTGGAC

ORF - retro_dnov_417 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.72 %
Parental protein coverage: 58.96 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLIGGNASA-EGPE-GEGTESTVITGVDIVMN-HHQE-PFTKEAYKKYIKDYMKSIKGKL-EEQRPERV-K
L.GG.ASA..GP...EG...T...G.DIV.N.H.QE.P.............MKSIKG.L.E.Q..ERV..
RetrocopyLTGGTASA<QGPR<AEGIAGTAPAGADIVINHHSQE>PASQKKPTRST*KMMKSIKGQL<EDQSSERV<N
ParentalSFMTGAAEQIKHILANFNNYQFFIGENMNPDG-MVALLD
SFMTGAAEQI.HILA.FNN..FFIGENM.PDG..VALLD
RetrocopySFMTGAAEQI-HILAIFNNHLFFIGENMSPDGVVVALLD

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 .19 RPM 181 .44 RPM
SRP012922_cerebellum 0 .00 RPM 63 .51 RPM
SRP012922_heart 0 .00 RPM 91 .19 RPM
SRP012922_kidney 0 .00 RPM 265 .86 RPM
SRP012922_liver 0 .00 RPM 112 .23 RPM
SRP012922_lung 0 .00 RPM 210 .30 RPM
SRP012922_quadricep_muscle 0 .00 RPM 308 .78 RPM
SRP012922_spleen 0 .00 RPM 310 .30 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_417 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 34 parental genes, and 252 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000065312 retrocopies
Ailuropoda melanoleuca ENSAMEG000000130228 retrocopies
Bos taurus ENSBTAG000000101562 retrocopies
Canis familiaris ENSCAFG0000000453310 retrocopies
Callithrix jacchus ENSCJAG000000192292 retrocopies
Cavia porcellus ENSCPOG0000000927812 retrocopies
Dasypus novemcinctus ENSDNOG00000000653 22 retrocopies
Dipodomys ordii ENSDORG000000085182 retrocopies
Equus caballus ENSECAG000000183483 retrocopies
Echinops telfairi ENSETEG000000030913 retrocopies
Felis catus ENSFCAG000000021078 retrocopies
Homo sapiens ENSG0000013311213 retrocopies
Gorilla gorilla ENSGGOG0000000168412 retrocopies
Latimeria chalumnae ENSLACG000000043062 retrocopies
Loxodonta africana ENSLAFG000000217407 retrocopies
Microcebus murinus ENSMICG000000020279 retrocopies
Myotis lucifugus ENSMLUG000000177091 retrocopy
Macaca mulatta ENSMMUG000000229792 retrocopies
Monodelphis domestica ENSMODG000000149402 retrocopies
Mustela putorius furoENSMPUG0000000164010 retrocopies
Mus musculus ENSMUSG000000601268 retrocopies
Nomascus leucogenys ENSNLEG000000021088 retrocopies
Oryctolagus cuniculus ENSOCUG000000236922 retrocopies
Otolemur garnettii ENSOGAG0000001252320 retrocopies
Procavia capensis ENSPCAG000000162283 retrocopies
Pongo abelii ENSPPYG000000053355 retrocopies
Pteropus vampyrus ENSPVAG0000000319115 retrocopies
Rattus norvegicus ENSRNOG000000010497 retrocopies
Sorex araneus ENSSARG000000093191 retrocopy
Sarcophilus harrisii ENSSHAG000000015451 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000069317 retrocopies
Tupaia belangeri ENSTBEG0000001353925 retrocopies
Tarsius syrichta ENSTSYG0000000316013 retrocopies
Vicugna pacos ENSVPAG000000084725 retrocopies



Copyright © RetrogeneDB 2014-2017