RetrogeneDB ID: | retro_pabe_609 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 10:72500108..72500809(-) | ||
| Located in intron of: | ENSPPYG00000002410 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TATDN1 | ||
| Ensembl ID: | ENSPPYG00000018868 | ||
| Aliases: | None | ||
| Description: | TatD DNase domain containing 1 [Source:HGNC Symbol;Acc:24220] |
Retrocopy-Parental alignment summary:
>retro_pabe_609
AAACAAATCATATGTTTTTTCAGCACAGTTGGATGTCATCCTACAAGATGTGGTGAATTTGAAAAGAATAACCCTGATCT
TTACTTAAAGAGTGCTAAATCTTGCTGAAAACAATAAAGGGGAAAGTTGTGGCAATAGGAGAATGTGGACTTGATTTTGA
CTGAACCTGCAGTTTTGTCCCAAAGATACTCAACTCGAAATATTGTGAAAAACAGTTTGAACTGTCAGAACAAACAAAAT
TACCAATGTTTCTTCATTGTCGAAACTCACATGCTGAATTTTTGGACATAATTAAAAGAAATAGAGATCGGTGTGTAGGG
GGAGTGGTGCACTCATTTGATGGTACCAAGGAAGCAGCAGCTGCTTTGATTGACTTGGATCTTTATATAGGATTTAATGG
TTGCTCACTGAAAACTGAAACTAATTTGGAAGTTCTGAAGTCAATTCCTAGTGAAAAATTAATGATTGAGACAAATGCAC
CTTGGTGTGGAGTCAAAAGTACACATGCTGGATCAAAATATATAAAAACTGCATTTCCTACCAAAAAGAAGTGGGAAAGT
GGGCACTGCTTAAAAGACATAAATGAACTCTGCCATGTAATTCAAATATTGGAGATAACGTCAGCAGTGAGAGACGAGGA
TCCACTGGAATCAGCCAATACACTATATAACAATACTATGAAAGTATTTTTTCCTGGAATA
ORF - retro_pabe_609 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.38 % |
| Parental protein coverage: | 98.31 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KFIDMFFSTVGCHPTRCGEFEKNNPDLYLKELLN-LAENNKGKVVAIGECGLDFD-RLQFCPKDTQLKYF |
| K.I..FFSTVGCHPTRCGEFEKNNPDLYLK.....L....KGKVVAIGECGLDFD....F.PK....KY. | |
| Retrocopy | KQIICFFSTVGCHPTRCGEFEKNNPDLYLKSAKS<LLKTIKGKVVAIGECGLDFD*TCSFVPKILNSKYC |
| Parental | EKQFELSEQTKLPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGSKEAAAALIDLDLYIGFNGCSLKT |
| EKQFELSEQTKLPMFLHCRNSHAEFLDI.KRNRDRCVGGVVHSFDG.KEAAAALIDLDLYIGFNGCSLKT | |
| Retrocopy | EKQFELSEQTKLPMFLHCRNSHAEFLDIIKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKT |
| Parental | EANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSA |
| E.NLEVLKSIPSEKLMIET.APWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKD.NE.CH.IQILEI.SA | |
| Retrocopy | ETNLEVLKSIPSEKLMIETNAPWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKDINELCHVIQILEITSA |
| Parental | VRDEDPLELANTLYNNTIKVFFPGI |
| VRDEDPLE.ANTLYNNT.KVFFPGI | |
| Retrocopy | VRDEDPLESANTLYNNTMKVFFPGI |
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 | 1 .38 RPM | 6 .52 RPM |
| SRP007412_cerebellum | 2 .07 RPM | 8 .03 RPM |
| SRP007412_heart | 1 .17 RPM | 3 .64 RPM |
| SRP007412_kidney | 0 .96 RPM | 5 .60 RPM |
| SRP007412_liver | 0 .43 RPM | 2 .26 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_609 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_609 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_609 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_578 |
| Gorilla gorilla | retro_ggor_514 |
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000018868 | 1 retrocopy |
retro_pabe_609 ,
|
| Tarsius syrichta | ENSTSYG00000001819 | 1 retrocopy |