RetrogeneDB ID: | retro_dnov_413 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_4494:214853..215365(-) | ||
| Located in intron of: | ENSDNOG00000016059 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TMEM106A | ||
| Ensembl ID: | ENSDNOG00000006233 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 106A [Source:HGNC Symbol;Acc:28288] |
Retrocopy-Parental alignment summary:
>retro_dnov_413
AAGCTCTCTGTGTTCCTGGAAGTGCTTATTTGCCTGTTAGCCTCCTTCCTCATCACCTCACTGTCTTTTTTCTGTTTCCC
CAGACCATTGCTGTGCAGGTGCAGGCCTCAACTCTTCCCCGGTCTTTGACCCGATTGAGATCCACCTAAATGTAACAAAT
ATCTTCAACACCTCCAATAATAACTACTACCTCATCATAGTAACCCAGATGACCATCGAAGTTCTGCATCTATCCCTTAT
GGTAGGACACATTTCCAAAAGCCTCCTCCTACACATTGGCCTTTGGCCAATGAACACATGTTTTATGCTAAGGCCAGCAG
GATATGGGATGGAAACACATACAAAATCTGTACCTGGCTGAAAACCCCAGGCCATCATGTACTTTTGCACATCCAGAGCA
CCCAGCCCTGTTCATACCTGAGCCACTTGAAGCAGCTAGTTTTCCAGTGCTAAGAGTACATGGACCGCTGGCAAACACTT
CGATGCCCCACTTGCCAGCCCCTCACCTGCCA
AAGCTCTCTGTGTTCCTGGAAGTGCTTATTTGCCTGTTAGCCTCCTTCCTCATCACCTCACTGTCTTTTTTCTGTTTCCC
CAGACCATTGCTGTGCAGGTGCAGGCCTCAACTCTTCCCCGGTCTTTGACCCGATTGAGATCCACCTAAATGTAACAAAT
ATCTTCAACACCTCCAATAATAACTACTACCTCATCATAGTAACCCAGATGACCATCGAAGTTCTGCATCTATCCCTTAT
GGTAGGACACATTTCCAAAAGCCTCCTCCTACACATTGGCCTTTGGCCAATGAACACATGTTTTATGCTAAGGCCAGCAG
GATATGGGATGGAAACACATACAAAATCTGTACCTGGCTGAAAACCCCAGGCCATCATGTACTTTTGCACATCCAGAGCA
CCCAGCCCTGTTCATACCTGAGCCACTTGAAGCAGCTAGTTTTCCAGTGCTAAGAGTACATGGACCGCTGGCAAACACTT
CGATGCCCCACTTGCCAGCCCCTCACCTGCCA
ORF - retro_dnov_413 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.49 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | KLSVFLAVLICLLTSFLVV---FF-LFPRTITVQ-PAGLNSSAVAFDTTDIHLNITNILNISNSNYYPIT |
| KLSVFL.VLICLL.SFL.....FF.LFP.TI.VQ..AGLNSS.V.FD...IHLN.TNI.N.SN.NYY.I. | |
| Retrocopy | KLSVFLEVLICLLASFLITSLSFF<LFPQTIAVQ<GAGLNSSPV-FDPIEIHLNVTNIFNTSNNNYYLII |
| Parental | VTQLTIEVLHLSLVVGSISNSLLLHIG-PLASEQMFYAVASRIGDENTYKICTWPKIKVHHVLLQIQGTL |
| VTQ.TIEVLHLSL.VG.IS.SLLLHIG.PLA.E.MFYA.ASRI.D.NTYKICTW.K...HHVLL.IQ.T. | |
| Retrocopy | VTQMTIEVLHLSLMVGHISKSLLLHIG<PLANEHMFYAKASRIWDGNTYKICTWLKTPGHHVLLHIQSTQ |
| Parental | TCSYLSHSEQLVFQSYDYVD-CRGNTSVSHLPVPHLP |
| .CSYLSH..QLVFQ...Y.D....NTS..HLP.PHLP | |
| Retrocopy | PCSYLSHLKQLVFQC*EYMD<PLANTSMPHLPAPHLP |
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 .39 RPM | 3 .31 RPM |
| SRP012922_cerebellum | 1 .10 RPM | 1 .37 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .27 RPM | 41 .62 RPM |
| SRP012922_liver | 0 .31 RPM | 5 .42 RPM |
| SRP012922_lung | 0 .31 RPM | 4 .12 RPM |
| SRP012922_quadricep_muscle | 0 .35 RPM | 0 .00 RPM |
| SRP012922_spleen | 0 .46 RPM | 30 .45 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_413 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 | ENSDNOG00000006233 | 1 retrocopy |
retro_dnov_413 ,
|