RetrogeneDB ID: | retro_rnor_2106 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 4:226837049..226837642(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSRNOG00000048902 | ||
| Aliases: | None | ||
| Description: | Influenza virus NS1A binding protein (Predicted), isoform CRA_d; Protein Ivns1abp [Source:UniProtKB/TrEMBL;Acc:D4A0T2] |
Retrocopy-Parental alignment summary:
>retro_rnor_2106
AATGGTTCCCAATGGATATTTGATGAGATTTTTATTGAATCTTCTGTTGCCAAATTAAGTGCCTTGAGGAAAAGTGGGCA
GTTCTGTGATGTTTGACTTCAGGTCTGGGGCCATGAAATGCTAGCACATAGGGCAGTCCTGGCTTGAGGTAGCACCTATC
TATTTGAAATCTTTAATAGTGACAGTGACACATGTGGAGTTCCTCATGTAAAGTCGGGTGATCTCGATCCAGAAGCTCTC
GAAGTCTTGCTGAATTACGTATACACTGCTCAGTTGAAAGCTGATAAAGAATTTGTAAAAGACGTTCATTCTGCCACAAA
GAAACTGAAGATGGACGGAGTAAAGCAGGTCTAGGAGATTATTTACTCTCTAGAGCGGATGCTGCTAGCCAGCTCTCTTA
CCGAAGCTTTGCAAGTTGGATGGGAGACTCCCGTTAGTTGAATAGAGTTGACGCTTATATTCAGGAGCATTTGTTACAAA
TCTCAGAAGAGGAGGAGTTTCTTGAGCTTCAGAGACTAACGTTGGAGGTAGTGCTTGAAGATAATGTTTGCTTGCCCGGC
AATGGCAAATTGTACACAAAGTTTCAAACCTGG
ORF - retro_rnor_2106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.39 % |
| Parental protein coverage: | 89.59 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NGYLMFEDENFIESSVAKLNALRKSGQFCDVRLQVCGHEMLAHRAVLACCSPYLFEIFNSDSDPHGVSHV |
| NG.....DE.FIESSVAKL.ALRKSGQFCDV.LQV.GHEMLAHRAVLA..S.YLFEIFNSDSD..GV.HV | |
| Retrocopy | NGSQWIFDEIFIESSVAKLSALRKSGQFCDV*LQVWGHEMLAHRAVLA*GSTYLFEIFNSDSDTCGVPHV |
| Parental | KLDDLNPEAVEVLLNYAYTAQLKADKELVKDVYSAAKKLKMDRVKQV-CGDYLLSRMDVTSCISYRNFAS |
| K..DL.PEA.EVLLNY.YTAQLKADKE.VKDV.SA.KKLKMD.VKQV..GDYLLSR.D..S..SYR.FAS | |
| Retrocopy | KSGDLDPEALEVLLNYVYTAQLKADKEFVKDVHSATKKLKMDGVKQV<LGDYLLSRADAASQLSYRSFAS |
| Parental | CMGDSRLLNKVDAYIQEHLLQISEEEEFLKLPRLKLEVMLEDNVCLPSNGKLYTKVINW |
| .MGDSR.LN.VDAYIQEHLLQISEEEEFL.L.RL.LEV.LEDNVCLP.NGKLYTK...W | |
| Retrocopy | WMGDSR*LNRVDAYIQEHLLQISEEEEFLELQRLTLEVVLEDNVCLPGNGKLYTKFQTW |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 29 .69 RPM |
| SRP017611_kidney | 0 .00 RPM | 123 .51 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .94 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2106 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2106 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_2106 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000048902 | 2 retrocopies |
retro_rnor_2106 , retro_rnor_2832,
|