RetrogeneDB ID: | retro_pabe_2429 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 4:39246702..39247335(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HSD17B6 | ||
| Ensembl ID: | ENSPPYG00000004673 | ||
| Aliases: | None | ||
| Description: | hydroxysteroid (17-beta) dehydrogenase 6 [Source:HGNC Symbol;Acc:23316] |
Retrocopy-Parental alignment summary:
>retro_pabe_2429
CTCTGGAGACTGGTGAACAATGCAGGCATTCTTACACCAATTACCTTATGTGAGTGGCTGAACACTGAGGACTTTATGAA
TATGCTCAAGGTGAACCTCATTGGTGTGATCCAGGTGACCTTGAGCGTGCTTCCTTTGGTGAGGAGAGCACGGGGAAGAA
TTGTCAATGTCTCCAGCATTCTGGGAAGAGTTGCTTTCTTTGTAGAAGGCTACTGTGTCTCCAAGTATGGAGTGGAAGCC
TTTTCAGATATTCTGAGGCGTGAGATTCAACATTTTGGGGTGAAAATCAGCATAGATGAACTTGGCTACTTCAGAACAGG
AATGACAAACCTGACACAGTCCTTAGAGCGAATGAAGCAAAGTTGGAAAGAAGCCCCCAAGCACATTAAGGAGACCTATG
GACAGCATTTTGATGCCTTTTACAGTATCATGAAGGAAGGGCTGTTGAATTGTAGCACAAACCTGAACCTGGTCACTGAC
TGCATGGAACATGCTCTGACATTGGTGCATCCGCAAACTCGATATTCAGCTGGCTGGGATGCTAAATTTTTCTTCATCCC
TCTATCTTATTTACCTACATCACTGGCAGACTACATTTTGACTAGATCTTGGCCCAAACCAGCCCAGGCAGTC
ORF - retro_pabe_2429 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.28 % |
| Parental protein coverage: | 66.88 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LWGLVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLSMLPLVRRARGRIVNVSSILGRVAFFVGG |
| LW.LVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLS.LPLVRRARGRIVNVSSILGRVAFFV.G | |
| Retrocopy | LWRLVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLSVLPLVRRARGRIVNVSSILGRVAFFVEG |
| Parental | YCVSKYGVEAFSDILRREIQHFGVKISIVEPGYFRTGMTNLTQSLERMKQRWKEAPKHIKETYGQQYFDA |
| YCVSKYGVEAFSDILRREIQHFGVKISI.E.GYFRTGMTNLTQSLERMKQ.WKEAPKHIKETYG.Q.FDA | |
| Retrocopy | YCVSKYGVEAFSDILRREIQHFGVKISIDELGYFRTGMTNLTQSLERMKQSWKEAPKHIKETYG-QHFDA |
| Parental | FYSIMKEGLLNCSTNLNLVTDCMEHALTSVHPRTRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ |
| FYSIMKEGLLNCSTNLNLVTDCMEHALT.VHP.TRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ | |
| Retrocopy | FYSIMKEGLLNCSTNLNLVTDCMEHALTLVHPQTRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ |
| Parental | AV |
| AV | |
| Retrocopy | AV |
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 | 2 .65 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1 .09 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .09 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .40 RPM |
| SRP007412_liver | 0 .12 RPM | 218 .04 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2429 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2429 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2429 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000004673 | 1 retrocopy |
retro_pabe_2429 ,
|
| Tarsius syrichta | ENSTSYG00000013583 | 1 retrocopy |