RetrogeneDB ID: | retro_sscr_913 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 7:94720783..94721362(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RPL19 | ||
| Ensembl ID: | ENSSSCG00000017509 | ||
| Aliases: | None | ||
| Description: | ribosomal protein L19 [Source:HGNC Symbol;Acc:10312] |
Retrocopy-Parental alignment summary:
>retro_sscr_913
AGTATGCTCAGGCTTCAGAAGAGGTTGCCTCCAGTGTCCTCCACTGTGACAAAAAGAAAGGTGGTTGGACCTCAATGAGA
CGAATGAAATCACCAATGCCAATTCCCATCAGCAGATCCAGAAGCTTATCAAAGATAGGCTGATCATCCCGAAGCCTGTG
ACCGTCCATTCCTGGGCTTGATGCCAGAAAAACACCTTGGCCCATGGGAGGACAGGCATATGGGCATAGGTAAGTGGAAG
CGTACTGCCAATGCTCGAATGCCCAAGAAGGTAACTTGGATGAGAAGGATAAGAATTCTCTGCTGGCTGCTCAGAAGATA
TCATGAATCTAAGAAGATTGACCACCACATGTATCACAGCCTGTACCTGAAAGTGAAGGGTAATGTGTTCCAAAACAAGT
GAATTGTCATGGAACATATCCATAAGCTGAAAGCAGACAAAGCTCACAAGCTTCTGGTTGACCAGGCTGAGGCCTGCAGG
TCTAAGATCAAGGAAGCATGCAAGTGCCCTGAAGAGCTGCTCTAGGCCAAGAAGGAGGAAATCATCAAGACTCTGTCCAA
GAAGGGAGAGACCAAGAAA
ORF - retro_sscr_913 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.79 % |
| Parental protein coverage: | 99.49 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SMLRLQKRL-ASSVLRCGKKKV-WLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLA |
| SMLRLQKRL.ASSVL.C.KKK..WLD.NETNEI.NANS.QQI.KLIKD.LII.KPVTVHS.A.C.KNTLA | |
| Retrocopy | SMLRLQKRL<ASSVLHCDKKKG<WLDLNETNEITNANSHQQIQKLIKDRLIIPKPVTVHSWA*CQKNTLA |
| Parental | RRK-GRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYHSLYLKVKGNVFKNKRIL |
| .....RHMGIGK.K.TANARMP.KVTWMRR.RIL..LLRRY.ESKKID.HMYHSLYLKVKGNVF.NK.I. | |
| Retrocopy | HGR<DRHMGIGKWKRTANARMPKKVTWMRRIRILCWLLRRYHESKKIDHHMYHSLYLKVKGNVFQNK*IV |
| Parental | MEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK |
| MEHIHKLKADKA..KLL.DQAEA.RSK.KEA.K..EE.L.AKKEEIIKTLSK..ETKK | |
| Retrocopy | MEHIHKLKADKAH-KLLVDQAEACRSKIKEACKCPEELL*AKKEEIIKTLSKKGETKK |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 525 .48 RPM |
| SRP014902_testis | 0 .00 RPM | 666 .78 RPM |
| SRP018288_heart | 0 .00 RPM | 371 .71 RPM |
| SRP018288_kidney | 0 .00 RPM | 459 .13 RPM |
| SRP018288_liver | 0 .00 RPM | 408 .25 RPM |
| SRP018288_lung | 0 .00 RPM | 466 .87 RPM |
| SRP018856_adipose | 0 .00 RPM | 1144 .71 RPM |
| SRP035408_brain | 0 .00 RPM | 838 .41 RPM |
| SRP035408_liver | 0 .00 RPM | 664 .00 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_913 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_913 was not experimentally validated.