RetrogeneDB ID: | retro_dnov_2048 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_44423:4715..5586(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NIPAL1 | ||
| Ensembl ID: | ENSDNOG00000002047 | ||
| Aliases: | None | ||
| Description: | NIPA-like domain containing 1 [Source:HGNC Symbol;Acc:27194] |
Retrocopy-Parental alignment summary:
>retro_dnov_2048
GGCCTCCTGCGACTTGCCAGAAAAGGCTCCATGAGAGCAGGTCAAGGTGGCCATGCATATCTTAAAGAATGGCTGTGGTG
GGCTGCACTGCAATCAATGGGAGCTGGTGAGGTGGCCAACTTTGCAGCATATGCATTTGCTGCAGCCACATTAGTGACTC
CTTTGGGAGCTCTTGGTGTCTTAGAGAGTGCCATTCTTTCTTCATATTTTCTAAATGAAAGACTTAAATCTTCATGGGAA
AATTGTATGTTTGTTAAGTATTTTAGGGTCTACAGTTATGGTCATCCATGCTCCAAAAGAAGAGGAGATAGAGACCTTAA
ATGAAATGTTTCACAAACTAGGTGATCCAGGTTTTGTGGTCTTTGCAACACTTGTGGTCATTGTGTCTTTGATATTAATT
TTCGTGGTGGGACCTCGCCATGGACAGACAAACGTTCTTGTGTACCTAACAATCTGCTCCGTGATTGGAGTGTTTTCCGT
CTCCTGTGTGAAAGGCCTGGGCATCGCTATTAAAGAACTGTTTGCTGGAAAGCCTGTTCTGCGACACCCCCTGGCCTGGA
TTCTCCTGCTGAGCCTGATAGTATGTGTGAGCACACAGATTAATTATCTGAACAGGGCCTTGGACATATTCAACACTTCC
ATCATGACACCAATATATTATGTATTATTCACAACATCAGTTTTAACTTGTTCAGCTACTCTTTTTAAGGAGTGGCAAGA
CATGCCTGTTGATGATATCATTGGTACTTTGAGCGGCTTCCTTACCATCATTGTGGGGATATTTTTATTGCATGCTTTTA
AAGATGTCAGTTTTAGTCTAGCGAGTCTGCCATTGTCTTTTCGAAAAGATGAGAAAGCAACAAATGGTAAT
ORF - retro_dnov_2048 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.67 % |
| Parental protein coverage: | 71.25 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GLLQLAQRGVTRAGEGGHSYLKEWLWWAGLLLMGAGEAVNFAAYAFAPATLVTPLGALSVLISAILSSYF |
| GLL.LA..G..RAG.GGH.YLKEWLWWA.L..MGAGE..NFAAYAFA.ATLVTPLGAL.VL.SAILSSYF | |
| Retrocopy | GLLRLARKGSMRAGQGGHAYLKEWLWWAALQSMGAGEVANFAAYAFAAATLVTPLGALGVLESAILSSYF |
| Parental | LNEHL-NIHGKIGCILSILGSTVMAIHAPREEEVTSLHEMEMKLRDPEFISFAVIIIVISLVLILVVAPK |
| LNE.L.N.HGKI.C.LSILGSTVM.IHAP.EEE...L.EM..KL.DP.F..FA......SL.LI.VV.P. | |
| Retrocopy | LNERL>NLHGKIVCLLSILGSTVMVIHAPKEEEIETLNEMFHKLGDPGFVVFATLVVIVSLILIFVVGPR |
| Parental | KGQTNILVYISICSLIGAFSVSSVKGLGIAIKELLEWKPVYKHPLVFVLLAVLVLSVSTQINYLNKALDT |
| .GQTN.LVY..ICS.IG.FSVS.VKGLGIAIKEL...KPV..HPL...LL..L...VSTQINYLN.ALD. | |
| Retrocopy | HGQTNVLVYLTICSVIGVFSVSCVKGLGIAIKELFAGKPVLRHPLAWILLLSLIVCVSTQINYLNRALDI |
| Parental | FNTSLVTPIYYVFFTSMVVTCSAILFQEWYGMKAEDIIGTLSGFFTIISGIFLLHAFKNTDITWSQLTST |
| FNTS..TPIYYV.FT..V.TCSA.LF.EW..M...DIIGTLSGF.TII.GIFLLHAFK........L... | |
| Retrocopy | FNTSIMTPIYYVLFTTSVLTCSATLFKEWQDMPVDDIIGTLSGFLTIIVGIFLLHAFKDVSFSLASLPLS |
| Parental | AKKDMITLNGH |
| ..KD....NG. | |
| Retrocopy | FRKDEKATNGN |
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 | 10 .70 RPM | 6 .61 RPM |
| SRP012922_cerebellum | 6 .60 RPM | 0 .14 RPM |
| SRP012922_heart | 2 .55 RPM | 9 .51 RPM |
| SRP012922_kidney | 3 .83 RPM | 0 .00 RPM |
| SRP012922_liver | 3 .56 RPM | 0 .00 RPM |
| SRP012922_lung | 10 .54 RPM | 1 .83 RPM |
| SRP012922_quadricep_muscle | 6 .58 RPM | 0 .00 RPM |
| SRP012922_spleen | 6 .98 RPM | 1 .14 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_2048 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 7 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000002047 | 1 retrocopy |
retro_dnov_2048 ,
|
| Homo sapiens | ENSG00000163293 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000009006 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000018625 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000017377 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014714 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000016038 | 1 retrocopy |