RetrogeneDB ID:

retro_dnov_867

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_11592:78454..78891(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATXN7L3
Ensembl ID:ENSDNOG00000003379
Aliases:None
Description:ataxin 7-like 3 [Source:HGNC Symbol;Acc:25416]


Retrocopy-Parental alignment summary:






>retro_dnov_867
GAGGAATTTGAGATTATGGAACAGACAGGGATATTCATCTTTGAAAAGGTTCTCAACCAATGCAAGTGAAAGTAGTGTGT
TTACCCAATTGCAGCCACAGCATTGCTGCCTCCTGCTCTGCTCCCCATCTGGAGAAGTGCCTGGAAATGTGTGGAACAGC
AGCCGCAGCCTCCAGGTTGCCAAAAGCAACAGTATGAACAAGTCTGAAAGTGACCAAGTGGACGATGATGACATCAATGA
CAACGACTGCTCCTGTAGATCGAGAAGAAATCCAAGAAGAGAAACTTGTTACGAATGGCAATTCCACTTGAAGATCCAAG
TCTTAAAAACACAAAAACTGGGAGTTTAGCAATTCAGATCCTTTTAAGCATAACAACTCCACTGGAATGAACTATGGGAC
CCTGGAGCCAGAGTAGCTGTGTAGCCTGCTCACCACG

ORF - retro_dnov_867 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.71 %
Parental protein coverage: 81.42 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalKDFEIVDQPGLDIFGQVFNQWKSKECV-CPNCSRSIAASRFAPHLEKCLGMGR-NSSRIANRRIANSNNM
..FEI..Q.G..IF..V.NQ.K.K.CV..PNCS.SIAAS..APHLEKCL.M...NSSR......A.SN.M
RetrocopyEEFEIMEQTGIFIFEKVLNQCK*K*CV<LPNCSHSIAASCSAPHLEKCLEMCG<NSSR--SLQVAKSNSM
ParentalNKSESDQEDNDDINDNDWSYGS-EKKAKKR-KSDKNPNSPRRSKSLKHKNGELSNSDPFKYNNSTGISYE
NKSESDQ.D.DDINDND.S..S.EKK.KKR.K...N.NS..RSKS.KHKN.E.SNSDPFK.NNSTG..Y.
RetrocopyNKSESDQVDDDDINDNDCSCRS<EKKSKKR<KLVTNGNST*RSKS*KHKNWEFSNSDPFKHNNSTGMNYG
ParentalTLGPEELRSLLTT
TL.PE.L.SLLTT
RetrocopyTLEPE*LCSLLTT

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 6 .22 RPM
SRP012922_cerebellum 0 .00 RPM 10 .59 RPM
SRP012922_heart 0 .00 RPM 2 .32 RPM
SRP012922_kidney 0 .00 RPM 2 .46 RPM
SRP012922_liver 0 .00 RPM 3 .41 RPM
SRP012922_lung 0 .00 RPM 5 .65 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .21 RPM
SRP012922_spleen 0 .00 RPM 4 .92 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_867 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 5 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000003379 13 retrocopies
Homo sapiens ENSG000000871521 retrocopy
Gorilla gorilla ENSGGOG000000109591 retrocopy
Myotis lucifugus ENSMLUG000000064161 retrocopy
Macaca mulatta ENSMMUG000000299351 retrocopy



Copyright © RetrogeneDB 2014-2017