RetrogeneDB ID:

retro_dnov_1583

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_239546:456..1169(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A28
Ensembl ID:ENSDNOG00000000849
Aliases:None
Description:solute carrier family 25 (mitochondrial iron transporter), member 28 [Source:HGNC Symbol;Acc:23472]


Retrocopy-Parental alignment summary:






>retro_dnov_1583
GAGGCCCTCTGGGGGGCTAGAAGAACGGAGGGCCTGAACATCTCAGCACCAGGCGCAGGTCCTGCCCATGCCCTCTGTTT
TTCCAGCTATTAAAAGTTAAGACCGACACTGAGTGATGTACTCCACCCTGGGGGCAGGAGCTGTGCTGCCAATGGTGCAG
CTGGGTATGTGGGCACATTACTTCATGGTGCAGCCATGAGTCCAGTGGAAGTGGTAAAGCAGAGGACACAGATGTACACA
GCTCACCTTACCACTGAGCAACAGAGTGTGTATGGGCAAGGTGGCAAAACGAAGGGGCCGGGGCCTTTCACTGCAGGTAC
ACCACCCAGCTCACCATGAATGTTCCCTTCCAAGCCACTCACTTCTTGACCCGTGAATTCCTGCAGGAGCACTTTAAGCC
CCCGAGACATACACCCCAGCTCCCATGTCCTCTCTGGAGCCTGTGCACAAGCTGTAGCTGCTGCTGCCACAACTCCACTG
GACATCTGCAAAACACTGCTCAACACCCAGAAATCCCCAGCTTTGAGCTCAAACATGACAGGACACATCAGAGGCATGGC
TGGTGCCTTCCAAGTAGGTGGGGTGACAGTCTACTTCCAAGGGTGCAGGCTAGAGTAATTTACCAAATCCCCTCCATGGC
CATTGAATGGGCTGTATATTAGTTTTTCAAATACCTAATCACTAAACGGCAAAAAGAGTGGGAGGCAGGCAAG

ORF - retro_dnov_1583 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.87 %
Parental protein coverage: 65.93 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEGLW--RPMRGLNVTATGAGPAHALYFACXXXXXXXXXDVIHPRANSHIANGAAGCVATLLHDAAMNPVE
E.LW..R...GLN..A.GAGPAHAL.F...........DV.HP...S..ANGAAG.V.TLLH.AAM.PVE
RetrocopyEALWGARRTEGLNISAPGAGPAHALCFSSY*KLRPTLSDVLHPGGRSCAANGAAGYVGTLLHGAAMSPVE
ParentalVVKQRMQMYNSPYHRVTD-CVRAVW---QNEGAGAFYRSYTTQLTMNVPFQAIHFMTYEFLQEHFNPQRR
VVKQR.QMY....H..T......VW...QNEGAGAF...YTTQLTMNVPFQA.HF.T.EFLQEHF.P.R.
RetrocopyVVKQRTQMYTA--HLTTE<ATECVWARWQNEGAGAFHCRYTTQLTMNVPFQATHFLTREFLQEHFKPPRH
Parental-YNP-SSHVLSGACAGAVAAAATTPLDVCKTLLNTQESLALNSNITGHITGMASAFRTVYQVGGVTAYFR
.Y.P.SSHVLSGACA.AVAAAATTPLD.CKTLLNTQ.S.AL.SN.TGHI.GMA.AF....QVGGVT.YF.
Retrocopy<YTP<SSHVLSGACAQAVAAAATTPLDICKTLLNTQKSPALSSNMTGHIRGMAGAF----QVGGVTVYFQ
ParentalG-VQARVIYQIPSTAIAWSVYEFFKYLITKRQEEWRAGK
G.VQARVIYQIPS.AI.W.VY.FFKYLITKRQ.EW.AGK
RetrocopyG<VQARVIYQIPSMAIEWAVY*FFKYLITKRQKEWEAGK

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 9 .14 RPM
SRP012922_cerebellum 0 .14 RPM 33 .40 RPM
SRP012922_heart 0 .00 RPM 10 .67 RPM
SRP012922_kidney 0 .00 RPM 13 .69 RPM
SRP012922_liver 0 .00 RPM 7 .90 RPM
SRP012922_lung 0 .00 RPM 27 .80 RPM
SRP012922_quadricep_muscle 0 .00 RPM 10 .04 RPM
SRP012922_spleen 0 .00 RPM 18 .66 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_1583 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000000849 1 retrocopy
retro_dnov_1583 ,


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