RetrogeneDB ID: | retro_pabe_1365 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 16:62024224..62025022(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMPO | ||
| Ensembl ID: | ENSPPYG00000004857 | ||
| Aliases: | None | ||
| Description: | thymopoietin [Source:HGNC Symbol;Acc:11875] |
Retrocopy-Parental alignment summary:
>retro_pabe_1365
ACAACCAGGAAGCTGTATGAGAAAAAGCTTTTGAAACTGAGGGAGCAAGGAACAGAATCAAGATCTTCTCCTTCAGCAAC
AATTTCTTCTTCAGCAGAAAATACAAGGCAGAATGGAAGTAATGATTCTGACAGATACAGTGACAATGAAGAAGACTCTA
AAATAGAGCTCAAGTTTGAGAAGAGAGAACCGCTAAAGAGCGGAGTAAAGACTCCAGTAACCCTCGAGCAAAGAAGAGTT
GAGCACGAGAGCTATTCTCAAGCTGGAATAACTGGGACTGAATGGACAAGTGGATCTTCAAAAGGTGGACCTCTGCAGGC
ATTATTAACTAGGGAATCTACAAGAGGGTCAAGAAGAACTCCAAGGAAAAGGGTGCACACTTCAGAATATTTTCCTATAG
ATGGAGCAGTAATTTCAGCGAGGACTCCCATAGCTGAAACTATAATGGCTTCAAACAACGAATCCTTAGTTGTCAATAGG
GTGACTGGAAACTTCAAGCATGCATTTCCTATTCTGCCGGTCACTGAATTCTCAGACATACCCAGAAGAACACCAAAGAA
ACCATTGACAAGAGCTGAAGTGGGAGAAAAAACACAGGAAAGAAGAGTAGAAAGGGATATTCTTAAGGAAATGTTCCCCT
ATGAAGCAGCTACACCAACAAGAATTAGTGCTAGTTGCCACAGAAAAATCAAAGGAGCTGCAGGCGGGCCATTAGAACTC
AGTGATTTGAGGATGGAGGAGTCGTTTTCATCTGCATATGTTCCTAAGTATGTTCCCTTGGCAGATGTCAAGTGAGAA
ORF - retro_pabe_1365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.43 % |
| Parental protein coverage: | 58.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSKIELKLEKREPLKGRA |
| TTRKLYEKKLLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRYSDNEEDSKIELK.EKREPLK... | |
| Retrocopy | TTRKLYEKKLLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYSDNEEDSKIELKFEKREPLKSGV |
| Parental | KTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVETSEHFRIDGPVI |
| KTPVTL.QRRVEH..SYSQAGIT.TEWTSGSSKGGPLQA.LTRESTRGSRRTPRKRV.TSE.F.IDG.VI | |
| Retrocopy | KTPVTLEQRRVEH-ESYSQAGITGTEWTSGSSKGGPLQALLTRESTRGSRRTPRKRVHTSEYFPIDGAVI |
| Parental | SESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGEKTEERRVERDIL |
| S..TPIAETIMAS.NESLVVNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVGEKT.ERRVERDIL | |
| Retrocopy | SARTPIAETIMASNNESLVVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGEKTQERRVERDIL |
| Parental | KEMFPYEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPLADVKSE |
| KEMFPYEA.TPT.ISASC.R.IKGAAG.PLELSD.RMEESFSS.YVPKYVPLADVK.E | |
| Retrocopy | KEMFPYEAATPTRISASCHRKIKGAAGGPLELSDLRMEESFSSAYVPKYVPLADVK*E |
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_prefrontal_cortex | 0 .00 RPM | 13 .44 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 23 .47 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .77 RPM |
| SRP007412_kidney | 0 .00 RPM | 12 .93 RPM |
| SRP007412_liver | 0 .00 RPM | 8 .45 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1365 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1365 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1365 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1652 |
| Pan troglodytes | retro_ptro_1123 |
| Gorilla gorilla | retro_ggor_1247 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000004857 | 1 retrocopy |
retro_pabe_1365 ,
|
| Pan troglodytes | ENSPTRG00000005331 | 1 retrocopy |