RetrogeneDB ID: | retro_pabe_774 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 11:71366905..71367420(-) | ||
| Located in intron of: | ENSPPYG00000003695 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP1R1A | ||
| Ensembl ID: | ENSPPYG00000004608 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286] |
Retrocopy-Parental alignment summary:
>retro_pabe_774
GCCCAGCCCCGAGTCCCGCGGCCTTCCCTCCGACCACAGTGCCAGCCCAGCAGGTGCCACCCCAACCATGGAGCAAGACA
ACAGCCCCCAGACCCCGAGGGGGCAGAGCAGATTTGGACATGTCGCCCAATGCTGCCACCCTTGTGCTGACCAGTCATCC
CCAGAGAGAGATGAACACGGATCCTCGACCCACTTTGGTAATGTCTCCACAGCGACAGAAGATGACAAGGATCACACCCA
CAACGAGAGAGCTCCAGATGATGGCTGAACATCACCTGGGGCAACAGCAGCAAGGAGAGGCGCCTGAGAAAGCTGCTGAG
AGCACAGGGACCCAGGAAACCTGCCCACCCGGGATCACAGACACGGAAGTGGAGTCAAGGCTGGGCACCTTTGGGCCAGC
ACAAGAGCCTGCAGAATCTATCCCCACAACTCAGGAGAGAGGCAGTAAAAAATGCAGCACAAAGGAACCCTCGATCCATG
TACCACCACTGGATTCCCAGGAAGCCAGCTCGGTT
ORF - retro_pabe_774 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.0 % |
| Parental protein coverage: | 78.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AGPAAAAPAMEQDSSPRKIQFTVPLLEPHLDPEAAEQIRRRRP-TPATLVLTSDQSSPEVDEDRIPNPHL |
| A.P....P.......P..............DPE.AEQI...RP...ATLVLT...S.P.......P.P.. | |
| Retrocopy | AQPRVPRPSLRPQCQPSRCHPNHGARQQPPDPEGAEQIWTCRP<NAATLVLT---SHPQREMNTDPRP-- |
| Parental | STLAMSPRQRKKMTRITPTMKELQMMVEHHLGQQQQGEEPEGAAESTGTQESRPPGIPDTEVESRLGTSG |
| .TL.MSP.QR.KMTRITPT..ELQMM.EHHLGQQQQGE.PE.AAESTGTQE..PPGI.DTEVESRLGT.G | |
| Retrocopy | -TLVMSP-QRQKMTRITPTTRELQMMAEHHLGQQQQGEAPEKAAESTGTQETCPPGITDTEVESRLGTFG |
| Parental | TAKKPAESIPKTQERGSKEPSTKAPSTHIPPLDSKGANSV |
| .A..PAESIP.TQERGSK..STK.PS.H.PPLDS..A.SV | |
| Retrocopy | PAQEPAESIPTTQERGSKKCSTKEPSIHVPPLDSQEASSV |
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 | 15 .70 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 15 .69 RPM |
| SRP007412_heart | 0 .03 RPM | 7 .65 RPM |
| SRP007412_kidney | 0 .03 RPM | 90 .13 RPM |
| SRP007412_liver | 0 .00 RPM | 221 .16 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_774 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_774 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_774 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_896 |
| Pan troglodytes | retro_ptro_619 |
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 |
retro_pabe_774 ,
|
| Pan troglodytes | ENSPTRG00000005044 | 2 retrocopies | |
| 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,
|