RetrogeneDB ID: | retro_ptro_1138 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 16:44294744..44295124(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP1R1A | ||
| Ensembl ID: | ENSPTRG00000005044 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286] |
Retrocopy-Parental alignment summary:
>retro_ptro_1138
CCATTCTCTGCCACCCTCCTGCTCACCCATGACCTGTCATCCCCAGAACTAGATAAAGACGGCTCCCCATCCCACTTCTG
AAGCCCACTTTGGGAGTGTCTGCACTTCAAGGGAAGACAACAAGAATCACACCCACCAGGAAACAGCTCCAAAGTAGGCT
TGAACGTTGCATGGGACAACAGCAGCCAGGAGCGGAGCCCAAAGGAGCTGCTGTGAGCACAGGGACCCTGGAGTACTGCC
CAGCTGGGATCACAGACGCAACAGAGTTAATGCTGGGAACCTCTGGGACAGCACCAAAGCCCTCAGAAGCCATCCTTAAA
GCTCAGGAGAGAGGCAGTAAGGACCCCAGCAGAGGAACCCACCACCCCTATACCACCATT
ORF - retro_ptro_1138 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.46 % |
| Parental protein coverage: | 88.19 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PTPATLVLTSDQSSPEIDED-RIPNPHLKSTLAMSPRQRKKMTRITPTMKELQMMVEHHLGQQQQGEEPE |
| P..ATL.LT.D.SSPE.D.D.R.P.P.LK.TL..S..Q.K..TRITPT.K.LQ...E...GQQQ.G.EP. | |
| Retrocopy | PFSATLLLTHDLSSPELDKD<RLPIPLLKPTLGVSALQGKT-TRITPTRKQLQSRLERCMGQQQPGAEPK |
| Parental | GAAESTGTQESRPPGIPDTEVESRLGTSGTAKKPAECIPKTHERGSKEPS--TKEPSTHI |
| GAA.STGT.E..P.GI.D...E..LGTSGTA.KP.E.I.K..ERGSK.PS..T..P.T.I | |
| Retrocopy | GAAVSTGTLEYCPAGITDA-TELMLGTSGTAPKPSEAILKAQERGSKDPSRGTHHPYTTI |
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 | 21 .34 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 17 .75 RPM |
| SRP007412_heart | 0 .00 RPM | 23 .52 RPM |
| SRP007412_kidney | 0 .00 RPM | 38 .18 RPM |
| SRP007412_liver | 0 .00 RPM | 78 .17 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .11 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1138 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1138 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1138 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1633 |
| Gorilla gorilla | retro_ggor_1231 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 27 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Felis catus | ENSFCAG00000010159 | 1 retrocopy | |
| Homo sapiens | ENSG00000135447 | 2 retrocopies | |
| Gorilla gorilla | ENSGGOG00000008380 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000004608 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000005044 | 2 retrocopies |
retro_ptro_1138 , retro_ptro_619,
|
| Tupaia belangeri | ENSTBEG00000001193 | 20 retrocopies |
retro_tbel_1191, retro_tbel_1233, retro_tbel_1251, retro_tbel_1264, retro_tbel_138, retro_tbel_1881, retro_tbel_2036, retro_tbel_2437, retro_tbel_2574, retro_tbel_2720, retro_tbel_3243, retro_tbel_3316, retro_tbel_3377, retro_tbel_3380, retro_tbel_3414, retro_tbel_3426, retro_tbel_4551, retro_tbel_537, retro_tbel_669, retro_tbel_899,
|