RetrogeneDB ID: | retro_ptro_1379 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 19:57006452..57006766(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM50B | ||
| Ensembl ID: | ENSPTRG00000013869 | ||
| Aliases: | None | ||
| Description: | Pan troglodytes transmembrane protein 50B (TMEM50B), mRNA. [Source:RefSeq mRNA;Acc:NM_001246571] |
Retrocopy-Parental alignment summary:
>retro_ptro_1379
AGTGAGAGAAGAAATGTTGTGGCGTCTGTTGTGACAGGTATATTGTTTTTTACAGGCTGGTGGATAATGACGCAGCTGTG
GTGTATTGTAGGTCAGAACAGTTGAACCATGCCTTTCACACATGTGGTGTATTTCCCACATTGGCTTTCTTCATGATAAA
TGCTGTATCCAATGCTCAGGTGAGAGGTGATAGCTATGAAAGTGGCTGTATAGGAAGAACAGGTCCTTGAGTTTGGCTTT
TCGTTGGTTTCATGTTGATGTTTGGGGTACTTATTGCTTCCATGTGGATTCTTTTTGGTGCATATGTTACCCAA
ORF - retro_ptro_1379 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.05 % |
| Parental protein coverage: | 67.09 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SERRNAVASVVAGILFFTGWWIMI-DAAVVYPKPEQLNHAFHTCGVFSTLAFFMINAVSNAQVRGDSYES |
| SERRN.VASVV.GILFFTG.W....DAAVVY...EQLNHAFHTCGVF.TLAFFMINAVSNAQVRGDSYES | |
| Retrocopy | SERRNVVASVVTGILFFTG-WWIM<DAAVVYCRSEQLNHAFHTCGVFPTLAFFMINAVSNAQVRGDSYES |
| Parental | GCLGRTGARVWLFIGFMLMFGSLIASMWILFGAYVTQ |
| GC.GRTG..VWLF.GFMLMFG.LIASMWILFGAYVTQ | |
| Retrocopy | GCIGRTGP*VWLFVGFMLMFGVLIASMWILFGAYVTQ |
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 .55 RPM | 14 .14 RPM |
| SRP007412_cerebellum | 0 .61 RPM | 34 .02 RPM |
| SRP007412_heart | 0 .58 RPM | 15 .16 RPM |
| SRP007412_kidney | 0 .97 RPM | 24 .95 RPM |
| SRP007412_liver | 0 .16 RPM | 11 .36 RPM |
| SRP007412_testis | 1 .26 RPM | 50 .37 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1379 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1379 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1379 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2066 |
| Gorilla gorilla | retro_ggor_1487 |
| Pongo abelii | retro_pabe_1679 |
| Macaca mulatta | retro_mmul_1408 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000003928 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000034844 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000012388 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000003887 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000013869 | 1 retrocopy |
retro_ptro_1379 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000023740 | 1 retrocopy |