RetrogeneDB ID: | retro_ptro_1870 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 3:28866134..28866434(-) | ||
| Located in intron of: | ENSPTRG00000030289 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM96A | ||
| Ensembl ID: | ENSPTRG00000007153 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235] |
Retrocopy-Parental alignment summary:
>retro_ptro_1870
GTTTTAGAAGAAGAAGGTCTAGAGCATTACACATTGTTTCCAACTATCTGGAACCCAAAGAAGCCTAATACGTTAAAAGA
ACTCTAAGTGATAACAGAAAGTCAATTGTAGCGTCAGGACCTCAATGAAGAAGACTCTCTGGTTATTATCAGGTTCACAC
ACCACAGTATCTCATTGTTTGGCGACTGTTATTAGGCTTTCCTTAAGAGCAAACTTGAGTGGAGTTTACCTTGTAAACTT
ACATTGGAAATTTACATTACTGAAGGAACCCACTAGAAAGAAGACCTCACTAAGAAGCAG
ORF - retro_ptro_1870 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.31 % |
| Parental protein coverage: | 63.12 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | IMEEKALEVYDLIRTIRDPEKPNTLEELEVVSESCVEVQEINEEEYLVIIRFT-PTVPHCSLATLIGLCL |
| ..EE..LE.Y.L..TI..P.KPNTL.EL.V..ES....Q..NEE..LVIIRFT..TV.HC.LAT.I.L.L | |
| Retrocopy | VLEEEGLEHYTLFPTIWNPKKPNTLKEL*VITESQL*RQDLNEEDSLVIIRFT>TTVSHC-LATVIRLSL |
| Parental | RV-KLQRCLPFKHKLEIYISEGTHSTEEDINKQ |
| R..KL...LP.K..LEIYI.EGTH..E....KQ | |
| Retrocopy | RA<KLEWSLPCKLTLEIYITEGTH*KEDLTKKQ |
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 .02 RPM | 5 .86 RPM |
| SRP007412_cerebellum | 0 .07 RPM | 5 .88 RPM |
| SRP007412_heart | 0 .03 RPM | 10 .08 RPM |
| SRP007412_kidney | 0 .00 RPM | 20 .08 RPM |
| SRP007412_liver | 0 .00 RPM | 34 .67 RPM |
| SRP007412_testis | 0 .00 RPM | 5 .48 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1870 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1870 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1870 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2763 |
| Gorilla gorilla | retro_ggor_1921 |
| Bos taurus | retro_btau_984 |
| Equus caballus | retro_ecab_364 |