RetrogeneDB ID: | retro_dnov_1019 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_13579:4166..4856(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SCNM1 | ||
| Ensembl ID: | ENSDNOG00000004323 | ||
| Aliases: | None | ||
| Description: | sodium channel modifier 1 [Source:HGNC Symbol;Acc:23136] |
Retrocopy-Parental alignment summary:
>retro_dnov_1019
ATGTCTTTCAAGAGGGAAGGGGACGATGGGAGTTAACTCAGTGTGCTCAAAACACAAAAAGTCGGTGACTTTTTGGCCAG
TAATATTCCAGAGAATGAGGCACTGATGCTGCGGGATGGACGCTTTGCTTGTGTCATCTGCCCACACCAGCCTGTACTGG
ACACCCTGGCCATGATGACTGACCACTGTGCAGGCAAGAAACGTCGGATCAGCTTGCAGCTGTTCTATGGGCCAAAAGCA
GCCAGATAGGGGAATGGAGCAGAATCCAAAATAGGAGAATGAATTGAGGAGGGAGGAGACCAAATCTGAGGCTCCTCTGC
TGGCCCAACCTCGGTTTACCACCCAGGGTGCTCTGCACAGAGCCCCCCACTTGAACAGTTGCTGCCGCCGCAAGTACAGA
CCAGAAGCCCCAGGTCCTTCTGTCTCCCGTTCCCCTTTGCCACCCCCAGAAGTTGAATTCCACAGCAGGAAGATCAGCAG
GGAACCTGAGCCCGGGACTAACCCACAGGCCAAGGAGTCAGCAACTGCCTCGGCGCCTCCACCCATGAGCCCACAGGAAG
ATAAGCCCTGGATCATTACCTCACCGTTCAAAGCTCTGGATGGATCCCATATGGACGAGGTCGATAGGTGAAAGATGGCA
ACGTTGAGTTTGACTCTGATCAGAAAGAACCCCCTGGTCTCCCTTTGGAC
ORF - retro_dnov_1019 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.29 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSFKREGDDWSQLNVLKKRRVGDLLASYIPEDEALMLRDGRXXXXXXPHRPVL-TLAMLTAHRAGKKHLS |
| MSFKREGDD.S.L.VLK...VGD.LAS.IPE.EALMLRDGR......PH.PVL.TLAM.T.H.AGKK... | |
| Retrocopy | MSFKREGDDGS*LSVLKTQKVGDFLASNIPENEALMLRDGRFACVICPHQPVLDTLAMMTDHCAGKKRRI |
| Parental | SLQLFYG-KKQTGRGMEQNPKQQSELR-EETKSEAPLLAQTRFITQSALHRAPHYNSCCRRKYRPEAPGP |
| SLQLFYG..KQ..RGMEQNPK...ELR.EETKSEAPLLAQ.RF.TQ.ALHRAPH.NSCCRRKYRPEAPGP | |
| Retrocopy | SLQLFYG>QKQPDRGMEQNPK*ENELRREETKSEAPLLAQPRFTTQGALHRAPHLNSCCRRKYRPEAPGP |
| Parental | SVPHSALPPPEVECHSGKTSREPEPGAGPQANESATASAPPPMS-PTRRRALDHYLTLRSSGWIPDGRGR |
| SV..S.LPPPEVE.HS.K.SREPEPG..PQA.ESATASAPPPMS.PT.R.ALDHYLT..SSGWIP.GRGR | |
| Retrocopy | SVSRSPLPPPEVEFHSRKISREPEPGTNPQAKESATASAPPPMS<PTGR*ALDHYLTVQSSGWIPYGRGR |
| Parental | WVKDENVEFDSDEEEPPDLPLD |
| .VKD.NVEFDSD..EPP.LPLD | |
| Retrocopy | *VKDGNVEFDSDQKEPPGLPLD |
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 | 12 .83 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 26 .81 RPM |
| SRP012922_heart | 0 .00 RPM | 8 .12 RPM |
| SRP012922_kidney | 0 .00 RPM | 27 .11 RPM |
| SRP012922_liver | 0 .00 RPM | 5 .11 RPM |
| SRP012922_lung | 0 .00 RPM | 31 .77 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 12 .12 RPM |
| SRP012922_spleen | 0 .00 RPM | 21 .40 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_1019 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000004323 | 1 retrocopy |
retro_dnov_1019 ,
|
| Oryctolagus cuniculus | ENSOCUG00000026766 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000021092 | 1 retrocopy |