RetrogeneDB ID: | retro_pabe_832 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:32973080..32973749(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM98B | ||
| Ensembl ID: | ENSPPYG00000006336 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 98, member B [Source:HGNC Symbol;Acc:26773] |
Retrocopy-Parental alignment summary:
>retro_pabe_832
CTGCTGAAAATTAATTTAAATTTGAAACAGGCAGAACAACTGGAAAGAGTCAATGATGCTCTTTCCTGTGAACATGAGTG
CCTCCAGCGAATGCTATGAAATGATTAGATGCGGCAATACAGTCCGTTGGACGGTGTGATACAGCCAAGGTAAGAACAGA
TGACACAGCAAGAATTTACCAGCCTAAGTGTTATGCTTTGTCACCCAAGACAGCGATTATAATGGTGCATCTACTTGCTG
CTCATGATGATCTATCCAAGATCATTAGGACAAGCAGTGGAGCCAGCCGGAAGATGGCATGTGCCATTAATAAGGTGCTG
ATGGGAAGGGTGCCTGACAGGGAAGGCTGGCCAAATGAAATTGAACCACCACCCTCTGAAATGCCCCCTTGGCAAAGAGA
CAAGAGGGCAGTGGCGGAAGGGGTGGTTGGGGTGGTGGTCGTGGAGATAGAGGTGGTAGTAGAAGAGGCTGTGGGGGTGG
AAGTGGAAGAGGTGGCTGGCGTGGAGGAGGATGGGAAAGTGGTGGGGGAGAGGGAGGAAGGTAGTGAGGAGGAAGTGGGA
TGGAGGTGGTAAAGGAGGTTTCCAAGGCAGAGGAGATGGTGGTGGGAGGGGAGATTATGGTAGAAAAGATTATGGAGATC
CATATGGAGGAGGTGGTGATGGTGGTGGA
ORF - retro_pabe_832 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.96 % |
| Parental protein coverage: | 52.55 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LLKIDLNSEQAEQLERINDALSCEYECRRRML-MKRLDVTVQSFGWSDRAKVKTDDIARIYQPKRYALSP |
| LLKI.LN..QAEQLER.NDALSCE.EC..RML.MK.LD...QS.G..D.AKV.TDD.ARIYQPK.YALSP | |
| Retrocopy | LLKINLNLKQAEQLERVNDALSCEHECLQRML<MK*LDAAIQSVGRCDTAKVRTDDTARIYQPKCYALSP |
| Parental | KTTITMAHLLAAREDLSKIIRTSSGTSREKTACAINKVLMGRVPDRGGRPNEIEPPPPEMPPWQ-KRQEG |
| KT.I.M.HLLAA..DLSKIIRTSSG.SR.K.ACAINKVLMGRVPDR.G.PNEIEPPP.EMPPWQ.KRQEG | |
| Retrocopy | KTAIIMVHLLAAHDDLSKIIRTSSGASR-KMACAINKVLMGRVPDREGWPNEIEPPPSEMPPWQ<KRQEG |
| Parental | GGGRGGWGGGGG--GGSRGGGGGGGGRGGWGGGGGWLGGGGGGGGGWGGGG-GGG-RGGFQGRGDYGGRG |
| .GGRGGWGGG.G..GGSR.G.GGG.GRGGW..GGGW..GGG.GG...GG.G..GG..GGFQGRGD.GGRG | |
| Retrocopy | SGGRGGWGGGRGDRGGSRRGCGGGSGRGGW-RGGGWESGGGEGGR**GGSG<DGGGKGGFQGRGDGGGRG |
| Parental | GYGGRGGYGGRGYGDPYGGGGGG |
| .Y.GR..YG...YG...GG.GGG | |
| Retrocopy | DY-GRKDYGD-PYGG--GGDGGG |
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 | 18 .52 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 19 .58 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .56 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .15 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .47 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_832 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_832 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_832 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000019041 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000006336 | 1 retrocopy |
retro_pabe_832 ,
|
| Rattus norvegicus | ENSRNOG00000005366 | 1 retrocopy |