RetrogeneDB ID: | retro_dnov_438 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_470:11897..12477(+) | ||
| Located in intron of: | ENSDNOG00000012411 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CHAC1 | ||
| Ensembl ID: | ENSDNOG00000017531 | ||
| Aliases: | None | ||
| Description: | ChaC, cation transport regulator homolog 1 (E. coli) [Source:HGNC Symbol;Acc:28680] |
Retrocopy-Parental alignment summary:
>retro_dnov_438
GACCCTCCAGTGCTGTGGATTTTTGGGTACAGCTCCCTGGTGTGGAACCCAACTTCGCCTTCACAACAGCTGCGTGGGCT
TCATGTGTGGCCACAGCCGCCTCTACTGGCAGGGAGACATCTTCCACTGGGGCAGTGACAAGATGCCTGGCCATGTGGTG
ACCCTCCTTGAAGACTGTGATGAGCATTGTGCTTGGGGCATGGAACACCAGGTTTGAGGCGAGCAGGTGAATGAGGCCCT
GAAGTACCTGAACATGCATGAGGTGGTACTCAGTGGCTGAGACACCAAGCAGGTCACTTTCTGCCCCAGGACACCTCTGA
CCAGCCACTGAAGACCTTGGCCTACACGGCCACCCCACAGAACCCTGACTACCTGGGCCCTGTGCCTGGAAGCCATTGCC
ACAAAGATCCTGGTCTGCTGAGTCTTCTCAGGCCACAACCTGGCATACGTGTTGTGCCTGGAAGACTTCACACAGCTCTG
TGGGCTCCAAGTACATGACAAGTACCTGGCGGCGATGGTGGATGCCATGGGTATCATGCTGCCCTGCTCCTGCCTCACCA
AGCAGGCTCTGGCACTGGTC
ORF - retro_dnov_438 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.5 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | DRPALWIFGYGYVM-ERPDFAFS-DSQVDFVRDYSRRFWQRDTFHRGSDKMPGRVVTLLED-GEGCTWGV |
| D.P.LWIFGY.......P.FAF...S.V.F....SR..WQ.D.FH.GSDKMPG.VVTLLED..E.C.WG. | |
| Retrocopy | DPPVLWIFGYSSLV<VEPNFAFT<NSCVGFMCGHSRLYWQGDIFHWGSDKMPGHVVTLLEDCDEHCAWGM |
| Parental | AYQVRGEQVNEALKYLNVREAVLGGYDTKEVTFCP-QDTPDQPLKALAYVAT-PQNPGYLGPAPE-EAIA |
| ..QV.GEQVNEALKYLN..E.VL.G.DTK.VTFCP.QDT.DQPLK.LAY.AT.P..P...GP....EAIA | |
| Retrocopy | EHQV*GEQVNEALKYLNMHEVVLSG*DTKQVTFCP<QDTSDQPLKTLAYTAT<PTEP*LPGPCAW<EAIA |
| Parental | TQILACRGFSGHNLEYLLRLADFMQLCGPQAQDEHLEAIVDAVGTKLPCFCPTEQALALV |
| T.IL.C..FSGHNL.Y.L.L.DF.QLCG.Q..D..L.A.VDA.G..LPC.C.T.QALALV | |
| Retrocopy | TKILVC*VFSGHNLAYVLCLEDFTQLCGLQVHDKYLAAMVDAMGIMLPCSCLTKQALALV |
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 .58 RPM | 1 .36 RPM |
| SRP012922_cerebellum | 0 .14 RPM | 3 .57 RPM |
| SRP012922_heart | 0 .23 RPM | 1 .16 RPM |
| SRP012922_kidney | 0 .00 RPM | 1 .10 RPM |
| SRP012922_liver | 0 .00 RPM | 1 .55 RPM |
| SRP012922_lung | 0 .61 RPM | 2 .75 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .17 RPM |
| SRP012922_spleen | 0 .23 RPM | 0 .46 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_438 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000017531 | 1 retrocopy |
retro_dnov_438 ,
|
| Otolemur garnettii | ENSOGAG00000024541 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000011476 | 2 retrocopies |