RetrogeneDB ID: | retro_rnor_709 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 10:73799138..73799759(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000027511 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Taf11 | ||
| Ensembl ID: | ENSRNOG00000024601 | ||
| Aliases: | None | ||
| Description: | Transcription initiation factor TFIID subunit 11 [Source:UniProtKB/Swiss-Prot;Acc:Q5U1X0] |
Retrocopy-Parental alignment summary:
>retro_rnor_709
ATGGAAAACCTTGGAGAGTCGCCCACGGACAAAGGCGGGGAGTCAGAGGAGTCGAGGGCTACTCCTGGGAACCCGTTAGC
GGCAGACACTGAGGGAATCCCTGAGGAAACCGATAGGGATGGAGACGTGGACTTGAAAGAAGCCGCGGCAGAGGAAAGGG
AGACCAAGAGTCAGGATGTCTCAGGTTTGACAGCAGTTGAGAGGGAAGACTCATTTCTTACTCCTGCAGCCAAAAAGCTG
AAACTAGAAACCAAAGACAAGAAGGAGAAGAAGCAGAAGGTGGACGAAGATGAGATTCAGAAGATGCAAATCCTGGTCTC
TTCTTTTTCTGAAGAGCAGCTGAACCGTTATGAAATGTATCGCCGGTCAGCTTTCCCGAAGGCAGCCATTAAAAGGCTGA
TCCAGTCCATCACTGGCACCTCTGTGTCTCAGAATGTTGTGATCGCCATGTCTGGCATTTCTAAAGTTTTTGTCGGGGAG
GTGGTAGAAGAAGCCCTGGATGTGTGTGAGAAATGGGGAGAAATGCCACCCCTGCAGCCCAAGCACATGAGGGAGGCCGT
GCGGAGGTTGAAGTCCAAGGGGCAAATCCCCAGCTCAAAGCACAAGAAAATCACCTTCTTC
ORF - retro_rnor_709 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.57 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDNLGESPTDKAGEPGESEETRATPGAPVSADTEGIPEETDQVGDADSKEAAAEESELKSQDVSDVTAAE |
| M.NLGESPTDK....GESEE.RATPG.P..ADTEGIPEETD..GD.D.KEAAAEE.E.KSQDVS..TA.E | |
| Retrocopy | MENLGESPTDKG---GESEESRATPGNPLAADTEGIPEETDRDGDVDLKEAAAEERETKSQDVSGLTAVE |
| Parental | REDPSLLTPAAKKLKLDTKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS |
| RED.S.LTPAAKKLKL.TKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS | |
| Retrocopy | RED-SFLTPAAKKLKLETKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS |
| Parental | ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPNSKHKKITF |
| ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP.SKHKKITF | |
| Retrocopy | ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPSSKHKKITF |
| Parental | F |
| F | |
| Retrocopy | F |
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 | 1 .08 RPM | 9 .99 RPM |
| SRP017611_kidney | 3 .77 RPM | 12 .49 RPM |
| SRP017611_liver | 1 .82 RPM | 5 .45 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_709 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_709 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_709 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000015428 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000011482 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000002023 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000024601 | 1 retrocopy |
retro_rnor_709 ,
|