RetrogeneDB ID: | retro_mdom_1931 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:184506307..184507416(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STAU1 | ||
| Ensembl ID: | ENSMODG00000016276 | ||
| Aliases: | None | ||
| Description: | staufen double-stranded RNA binding protein 1 [Source:HGNC Symbol;Acc:11370] |
Retrocopy-Parental alignment summary:
>retro_mdom_1931
CAGGTCTCCAGGGAGAGTGGCCCACCTCACATGAAGACTTTTGTGACAAAGGTGTCAGTTGGTGAATTCATGGGTGAAGG
TGAAAGAAAAAGCAAGAAGATTTCAAAGAAAAATGGTGCTATAGCTGTCCTTGAGGGACTAAAGAAATTACCTCCTCTTC
GAAAAGTTGAGAAAATGAAGCCACAAATTAAAAAGAAAACAAAATCTATAGTTAAGCTACCAAATATGGTCAAGGAATGA
ATCCAATTATCCAACTTGCCCAGATCCAACAGGTCAAAAAAGATAAGGAGCCTGAATACATGCTTCTCACTGAGCGAGGT
CTTCCTCATCGCAGGGAGTTTGTGAGGCAGGTCAAAGTTGGTGGCCATACTGCTGAAGGAATGGGCATGAATAAGAAGGT
AGAAAAGCGCAATGCAGCTGAAAATATGTTAGAGATCCTAGGCTTCAAAGGCCCCCCAAGCCCAGCCCCCTAATCCAGCA
GTGAAGACAGAAGAAAAAACCCCAGTAAAGGTGATAGAAGACAAGTTATCTTTTTTGAGCCCAACTCTGGTGATGAAAAT
GTGACCCGTAATAAGAAAGATGAAATTAGGATGCCTTATCTCAGTCATCAGCAACTTTCAGCAGGAATTCTTCCCGTGGT
GCCTGAAGTGGCACAGGCTGTAGGAGTCAAGCAAGGACATCATACCAAAAAGTTTATCAAGTTAGCTCTGAATCCTGCCA
AGGCATCTATCACAGCCATGATTGCTAGAGAGCTATTGTATGGGGGGACCTCCCCAACAGCTGAGACCATTTTAAAGAAT
AACATCTCCTCAGGCCATGTCTCCCACAGGCCACTTACTGGACCCTCTGAACAACTGGATTATCTTTCCAATGTCCAGGG
AATACAGGTGGAATACAAAGACTTTCCAAAAAACAACAAGAATGAGTTTGTCTCTCTTATAAATTGTTCCTCTCAGCTAT
GTCTGATCAGCCATGGAATTGGAAAGTATGTGGCATCCTGCCATGACATGGCTGCATTGAACATTTTAAAGTTGCTGTCT
GAGGTGGACCAACAAAGTCCAGAGATGCCAAGAACATAAAATGGACCAATGTCTGTGTGTGGGAGGTGC
ORF - retro_mdom_1931 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.95 % |
| Parental protein coverage: | 56.05 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | EVTRESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELKKLPPLPTVEKMKPRIKKKTKSI |
| .V.RESGPPHMK.FVTKVSVGEFMGEGE.KSKKISKKN.AIAVLE.LKK...LP...K.........K.. | |
| Retrocopy | QVSRESGPPHMKTFVTKVSVGEFMGEGERKSKKISKKNGAIAVLEGLKK---LPPLRKVEKMKPQIKKKT |
| Parental | VKLQTSP-EYGQGMNPISRLAQIQQAKKDKEPEYMLLTERGLPRRREFVMQVKVGGHTAEGMGTNKKVAK |
| ......P..YGQGMNPI..LAQIQQ.KKDKEPEYMLLTERGLP.RREFV.QVKVGGHTAEGMG.NKKV.K | |
| Retrocopy | KSIVKLP<KYGQGMNPIIQLAQIQQVKKDKEPEYMLLTERGLPHRREFVRQVKVGGHTAEGMGMNKKVEK |
| Parental | RNAAENMLEILGFK-VPQAQPPKPALKTEEKT-PVKKPGDGRKVTFFEPNSGDENVTSNKEDEFRMPYLS |
| RNAAENMLEILGFK..PQAQPP.PA.KTEEKT.P.K..GD.R.V.FFEPNSGDENVT.NK.DE.RMPYLS | |
| Retrocopy | RNAAENMLEILGFK>APQAQPPNPAVKTEEKT<PSK--GDRRQVIFFEPNSGDENVTRNKKDEIRMPYLS |
| Parental | HQQLPAGILPMVPEVAQAVGVNQGHHTKEFTRVAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSG |
| HQQL.AGILP.VPEVAQAVGV.QGHHTK.F...A.NPAKA..TAMIARELLYGGTSPTAETILKNNISSG | |
| Retrocopy | HQQLSAGILPVVPEVAQAVGVKQGHHTKKFIKLALNPAKASITAMIARELLYGGTSPTAETILKNNISSG |
| Parental | HVPHGPLTRPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNI |
| HV.H.PLT.PSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQ..LISHGIGK.V.SCHDMAALNI | |
| Retrocopy | HVSHRPLTGPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQLCLISHGIGKYVASCHDMAALNI |
| Parental | LKLLSELDQQSTEMPRTGNGPMSVCGRC |
| LKLLSE.DQQS.EMPRT.NGPMSVCGRC | |
| Retrocopy | LKLLSEVDQQSPEMPRT*NGPMSVCGRC |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 631 .86 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 678 .37 RPM |
| SRP007412_heart | 0 .00 RPM | 607 .23 RPM |
| SRP007412_kidney | 0 .00 RPM | 812 .49 RPM |
| SRP007412_liver | 0 .00 RPM | 504 .50 RPM |
| SRP007412_testis | 0 .00 RPM | 328 .44 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1931 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1931 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016233 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016276 | 1 retrocopy |
retro_mdom_1931 ,
|
| Sus scrofa | ENSSSCG00000027444 | 1 retrocopy |