RetrogeneDB ID: | retro_ggor_2001 | ||
Retrocopy location | Organism: | Gorilla (Gorilla gorilla) | |
| Coordinates: | 3:180478434..180479661(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LRRFIP1 | ||
| Ensembl ID: | ENSGGOG00000008411 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ggor_2001
ATCAGGGAAATCAAGGACTCTCTAGCAGAAGTTGAAGAGAAATATAAGAAGGTTATGTTTTCCAATGCTCAGCTAGACAA
TGAAAAGACAAACTTCATTTACCAAGTTGACCCCCTGAAAGATATGTTGCTGGAGCTTGAAGAACAGCTGGCTGAATCTA
GGCGGCAGTACGAAGAGAAAAACAAAGAATTTGAAAGGGAAAAACACGCCCACAGTATACTGCAGTTTCAGTTTGCTGAA
GTCAAGGAGGCCCTGAAGCAAACAGAGGAAATGCTCGAGAAACATGGAATAATCCTAAATTCAGAAATAGTTACCAATGG
AGACACTTCCGACACTCTCAGTAATGTTGGATACCAAGATCCAACCAAGATGACGAAAGAAGAGTTAAATGCCCTCAAGT
CGACAGGGGATGGGACCCTAGGAAAGCCAGTGAAGTGGAGGTGAAGAATGAAATCGTGGCGAATGTGGGTAAAAGAGATA
TCTTGCACAATACTGAGAAAGAACAACACACAGAGGACACAGTGAAGGATTGTGTGGACATAGAGGTATTCACTGCTGGT
GAGAATGCCGAGGACCAGAAATCCTCTGAAGACACTGCCCCATTCCTAGGAACCTTAGCAGGTGCTACCTATGAGGAACA
GGTTCAAAGCCAAATTCTTGAGAGCGCTTCTCTCCCTGAAAACACAGCACAGGTTGAGTCAAATGAGGTCATGGGGTGCA
CCAGATGACAGGACCAGAACTCCCCTTGAGCCATCCAACTGTTGGAGTGACTTAGATGGTGGGAGCCACACAGAGAATGT
GGGAGAGGCAGCGGTGACTCAGGTTGGAGAGCAGGCAGACACAGTGGCCTCATGTCCTTCAGGGCATAGTGATGACACAG
TTAATCATGATGACAGATGTATGGTAGAGGTCCCCCAAGAGTTAGAGACAAGCATAGGGCATAGTTTAGAGAAAGAATTC
ACCAACCAGGAAGCAGCTGAGCCCAAGGAGGTTCCAGTGCAGAGTACAGAAGCAGGTAGGGATCACAACGAAGAAGAGGG
TGAAGAAAAAGGATTAAGAGATGAGAAACCAATCAAGACAGAAGTTCCTGGTTCTCCAGCAGGAACTGAGAGCAAGGGTC
AGGAGGCGACAGGTCCAAGTACAGTAGACACTCAAAGTGAACCCTCAGATATGAAAGAGCCAGATGAAGAAAAGAATGAC
CAACAGGGAGAGGCATTGGACTCATCG
ORF - retro_ggor_2001 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.75 % |
| Parental protein coverage: | 50.62 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LKEMKDSLAEVEEKYKKAMVSNAQLDNEKTNFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHA |
| ..E.KDSLAEVEEKYKK.M.SNAQLDNEKTNF.YQVD.LKDMLLELEEQLAESRRQYEEKNKEFEREKHA | |
| Retrocopy | IREIKDSLAEVEEKYKKVMFSNAQLDNEKTNFIYQVDPLKDMLLELEEQLAESRRQYEEKNKEFEREKHA |
| Parental | HSILQFQFAEVKEALKQREEMLEKHGIILNSEIATNGETSDTLNNVGYQGPTKMTKEELNALKSTGDGTL |
| HSILQFQFAEVKEALKQ.EEMLEKHGIILNSEI.TNG.TSDTL.NVGYQ.PTKMTKEELNALKSTGDGTL | |
| Retrocopy | HSILQFQFAEVKEALKQTEEMLEKHGIILNSEIVTNGDTSDTLSNVGYQDPTKMTKEELNALKSTGDGTL |
| Parental | GR-ASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDCVDIEVFPAGENTEDQKSSEDTAPFLGTLAGA |
| G..ASEVEVKNEIVANVGKR.ILHNTEKEQHTEDTVKDCVDIEVF.AGEN.EDQKSSEDTAPFLGTLAGA | |
| Retrocopy | GK<ASEVEVKNEIVANVGKRDILHNTEKEQHTEDTVKDCVDIEVFTAGENAEDQKSSEDTAPFLGTLAGA |
| Parental | TYEEQVQSQILESTSLPENTVQVESNEVL-GAPDDRTRTPLEPSNCWSDLDDGSHTENVGEAAVTQVEEQ |
| TYEEQVQSQILES.SLPENT.QVESNEV..GAPDDRTRTPLEPSNCWSDLD.GSHTENVGEAAVTQV.EQ | |
| Retrocopy | TYEEQVQSQILESASLPENTAQVESNEVM>GAPDDRTRTPLEPSNCWSDLDGGSHTENVGEAAVTQVGEQ |
| Parental | AGTVASCPLGHSDDTVHHDDKCMVEVPQELETSTGHSLEKEFTNQEAAEPKEVPAHSTEVCRDHNEEEGE |
| A.TVASCP.GHSDDTV.HDD.CMVEVPQELETS.GHSLEKEFTNQEAAEPKEVP..STE..RDHNEEEGE | |
| Retrocopy | ADTVASCPSGHSDDTVNHDDRCMVEVPQELETSIGHSLEKEFTNQEAAEPKEVPVQSTEAGRDHNEEEGE |
| Parental | ETGLRDEKPIKTEVPGSPAGTEGNGQEAAGPSTVDTQNEPLDMKEPDEEKNDQQGEALDSS |
| E.GLRDEKPIKTEVPGSPAGTE..GQEA.GPSTVDTQ.EP.DMKEPDEEKNDQQGEALDSS | |
| Retrocopy | EKGLRDEKPIKTEVPGSPAGTESKGQEATGPSTVDTQSEPSDMKEPDEEKNDQQGEALDSS |
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 .96 RPM | 63 .78 RPM |
| SRP007412_cerebellum | 1 .02 RPM | 37 .07 RPM |
| SRP007412_heart | 1 .06 RPM | 51 .03 RPM |
| SRP007412_kidney | 1 .39 RPM | 106 .19 RPM |
| SRP007412_liver | 1 .00 RPM | 45 .69 RPM |
| SRP007412_testis | 7 .15 RPM | 19 .48 RPM |
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_2001 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ggor_2001 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2887 |
| Macaca mulatta | retro_mmul_1455 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000124831 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000008411 | 1 retrocopy |
retro_ggor_2001 ,
|
| Macaca mulatta | ENSMMUG00000003386 | 1 retrocopy |