RetrogeneDB ID: | retro_ptro_2473 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 6:117266141..117266470(-) | ||
| Located in intron of: | ENSPTRG00000018523 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NIP7 | ||
| Ensembl ID: | ENSPTRG00000008279 | ||
| Aliases: | None | ||
| Description: | 60S ribosome subunit biogenesis protein NIP7 homolog [Source:RefSeq peptide;Acc:NP_001233354] |
Retrocopy-Parental alignment summary:
>retro_ptro_2473
ACCTCCTTCAGAAAATTCACCAAGACCTACAAGTTTCAGTTGAACATCACAGCTCTGGATTACCCTGCATCCTATGCCAA
GTATAAAGTGTGGATAAAACCTGGAGCACAGTAGTCCTTTCTATATGGGGACAATATGTTGAAATCTGGTCTGAGTCAAA
TCACGAAAAATACTTCTCCTGGCCAGGAAGTGGTGGTGGCAGACATCCCTTTGGGTTTTGGGGTGGCAGCCACATCTACG
CAAGACTGCAGAAAAGGAGACCCCATCGATTTGTGGTATTTCATCAAGCAAACACTGGTGAATATGTGCGGCATGAAGAG
ACGGTGACT
ORF - retro_ptro_2473 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.81 % |
| Parental protein coverage: | 62.78 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TCFGKFTKTHKFRLHVTALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTSQYQGVVVYSMA |
| T.F.KFTKT.KF.L..TALDY.A.YAKYKVWIKPGA..SFLYG...LKSGL..IT.NTS..Q.VVV...A | |
| Retrocopy | TSFRKFTKTYKFQLNITALDYPASYAKYKVWIKPGAQ*SFLYGDNMLKSGLSQITKNTSPGQEVVV---A |
| Parental | DIPLGFGVAAKSTQDCRKVDPMAI-VVFHQADIGEYVRHEETLT |
| DIPLGFGVAA.STQDCRK.DP....VVFHQA..GEYVRHEET.T | |
| Retrocopy | DIPLGFGVAATSTQDCRKGDPIDL<VVFHQANTGEYVRHEETVT |
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 .05 RPM | 6 .51 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 5 .92 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .63 RPM |
| SRP007412_kidney | 0 .00 RPM | 9 .34 RPM |
| SRP007412_liver | 0 .00 RPM | 15 .12 RPM |
| SRP007412_testis | 0 .00 RPM | 47 .11 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2473 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2473 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_2473 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3648 |
| Gorilla gorilla | retro_ggor_2464 |
| Pongo abelii | retro_pabe_2995 |
| Macaca mulatta | retro_mmul_1801 |
| Callithrix jacchus | retro_cjac_2466 |