RetrogeneDB ID: | retro_rnor_1601 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 2:8705573..8706194(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ubxn1 | ||
| Ensembl ID: | ENSRNOG00000019666 | ||
| Aliases: | Ubxn1, 2B28, RGD1309471 | ||
| Description: | UBX domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q499N6] |
Retrocopy-Parental alignment summary:
>retro_rnor_1601
AGAGGAGAACAGACTGAGAGAATGTTGGGAATTGTGTCACAGAAGCAGCGGGAATGTGAAGAAAGAGAGAAGCGAGAAGC
TTTAGGACTAGAAAAGCAGCGGAGGAGACAAGGGCAAGAGCTATCAGCTTCACAACAGAAACCACAGGAAGACTAGGTGC
CCTGGGCTGCTGAGGAGCGCAGGAGGGAAAAGGCTGAAGAGTTAGTGGCCAGACAAAAGGTTCGAGAAAAAATTGAAAGG
GACAAAGCAGAGAGAGCCCAGAAGTATGCTGGTACTGTGGGTTCTCGGGCACCGTCGTCAGCAACAGATCCAGGTACTGT
TCCTTCTTCTCCCAGCCAGGAACCCCCTACTACGCAGGAATATGACCAATGTTGCATACAGGTTAGGCTGCCTGATGGGA
CTTCACTGACCCAAACCTTCCGGGCCCGGGAACAGCTGGCGGCTGTGAGGCTCTATGTGGAGCATCACCGTGGGGAAGAA
CCTGGACAGGACCAGGACCCTCTGCAGCTGCTCAGTGGCTTCCCCAGATGGGCTTTCTCAGAGGCTGACACGGAACAGCC
CCTGCAGAAATTGGGACTCATGCCTTCTGCTGTCCTCATCGTGGCCAAGAAGTGTCCCAGC
ORF - retro_rnor_1601 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.09 % |
| Parental protein coverage: | 69.7 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RQEQTKRMLELVAQKQREREEREEREALEREKQRRRQGQELSAARQKLQEDEIRRAAEERRREKAEELAA |
| R.EQT.RML..V.QKQRE.EERE.REAL..EKQRRRQGQELSA..QK.QED....AAEERRREKAEEL.A | |
| Retrocopy | RGEQTERMLGIVSQKQRECEEREKREALGLEKQRRRQGQELSASQQKPQED*VPWAAEERRREKAEELVA |
| Parental | RQRVREKIERDKAERAQKYGGTVGSRSSPPATDPGPVPSSPRQEPPTKREYDQCRIQVRLPDGTSLTQTF |
| RQ.VREKIERDKAERAQKY.GTVGSR....ATDPG.VPSSP.QEPPT..EYDQC.IQVRLPDGTSLTQTF | |
| Retrocopy | RQKVREKIERDKAERAQKYAGTVGSRAPSSATDPGTVPSSPSQEPPTTQEYDQCCIQVRLPDGTSLTQTF |
| Parental | RAREQLAAVRLYVELHRGEEPGQDQDPVQLLSGFPRRAFSEADMERPLQELGLVPSAVLIVAKKCPS |
| RAREQLAAVRLYVE.HRGEEPGQDQDP.QLLSGFPR.AFSEAD.E.PLQ.LGL.PSAVLIVAKKCPS | |
| Retrocopy | RAREQLAAVRLYVEHHRGEEPGQDQDPLQLLSGFPRWAFSEADTEQPLQKLGLMPSAVLIVAKKCPS |
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 | 48 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 69 .43 RPM |
| SRP017611_liver | 0 .00 RPM | 38 .66 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1601 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1601 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_1601 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000019666 | 1 retrocopy |
retro_rnor_1601 ,
|
| Sorex araneus | ENSSARG00000008689 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000007971 | 1 retrocopy |