RetrogeneDB ID: | retro_dnov_1000 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_132631:854..1457(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KCMF1 | ||
| Ensembl ID: | ENSDNOG00000006752 | ||
| Aliases: | None | ||
| Description: | potassium channel modulatory factor 1 [Source:HGNC Symbol;Acc:20589] |
Retrocopy-Parental alignment summary:
>retro_dnov_1000
CGGGCTTGCTTCTCCTAGAGTTCATGTCCTCCCAGCAGCGGGGAAGCCGCGGGTCCTGCAGCTGCGCTTTGTCTCGGTTC
TCAGGAGGGAGATGGTCCGCAGGGAGTCAGCTTCCCTCTTCCAGCCCTGCCGCTTCGCGGTCACAGCAACCGCAGGTGCA
GCTGCAGCTGGAGCGGCAGCGGGCCCGGGCACTCGGCGGCCGCTGGGGACCGCACTCCACGGGAGCCGGCGTGCCAACAC
CAGGAGTGTCACCACGACCGTCGCCGTCCACAGCGACAACCCAACCCAGCAACACAGAGAGCAGGCAGCAAACTCTCCAG
GAGCCACGGTTTCCTTTAACGAGGCTGCAGGAGCATAAAATGTCGGAACCAGGGCGCCAGTCCAAGGAAAGCGAGCGCGC
AGAGGGCAGCCTGTGTGTCCCAGAGCTCCCTCTGTCCACTTTAGTGCCGAGGCAAGCTCGTCATGAGACCAGGGTGAGCC
CGGAGGGGGGTGGGAGGTGGGAGGTTTTGGTGCTAAGGGCTGAGTAGATATTACGCCTTTAGATGTTGTTTCAGGAAACT
AAATTTAAAAGAGAGAAATAAAGGAGATGAGCCTCCACCTCCT
ORF - retro_dnov_1000 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.33 % |
| Parental protein coverage: | 52.76 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | RLSSSQSSYSPSNREAMDPIAAEL-LSQLSGVRRSAGGQLNSSGPSASQLQQLQMQLQLERQHAQA-ARQ |
| R...S.SS..PS..EA..P.AA.L.LS..SG.R.SAG.QL.SS.P.AS..QQ.Q.QLQLERQ.A.A..R. | |
| Retrocopy | RACFS*SSCPPSSGEAAGP-AAAL<LSRFSGGRWSAGSQLPSSSPAASRSQQPQVQLQLERQRARA<TRR |
| Parental | QLETARNATRRTNTSSVTTTI-TQSTATTNTANTESSQQTLQNSQFLLTRLNDPKMSETERQSMESERAD |
| .L.TA....RR.NT.SV.TT....STATT...NTES.QQTLQ...F.LTRL...KMSE..RQS.ESERA. | |
| Retrocopy | PLGTALHGSRRANTRSV-TTT>SPSTATTQPSNTESRQQTLQEPRFPLTRLQEHKMSEPGRQSKESERAE |
| Parental | RSLFVQELLLSTLV-REESSSSDEDDRG---EMADFGAMGCVDIMPLDVALEN-LNLKESNKGNEPPPP |
| .SL.V.EL.LSTLV..E.SSS.D....G...E...FGA.G.VDI.PLDV...N.LNLKE.NKG.EPPPP | |
| Retrocopy | GSLCVPELPLSTLV<AEASSS*DQGEPGGGWEVGGFGAKG*VDITPLDVVSGN<LNLKERNKGDEPPPP |
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 | 36 .95 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 31 .34 RPM |
| SRP012922_heart | 0 .00 RPM | 40 .14 RPM |
| SRP012922_kidney | 0 .00 RPM | 28 .47 RPM |
| SRP012922_liver | 0 .00 RPM | 19 .04 RPM |
| SRP012922_lung | 0 .92 RPM | 45 .21 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 112 .68 RPM |
| SRP012922_spleen | 1 .49 RPM | 49 .33 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_1000 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 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000005786 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000006752 | 2 retrocopies |
retro_dnov_1000 , retro_dnov_2063,
|
| Echinops telfairi | ENSETEG00000001809 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000000979 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000015567 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000034863 | 2 retrocopies | |
| Vicugna pacos | ENSVPAG00000010386 | 1 retrocopy |