RetrogeneDB ID: | retro_ptro_688 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 12:44234486..44236044(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLEKHA8 | ||
| Ensembl ID: | ENSPTRG00000019036 | ||
| Aliases: | None | ||
| Description: | Pan troglodytes pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 (PLEKHA8), mRNA. [Source:RefSeq mRNA;Acc:NM_001199079] |
Retrocopy-Parental alignment summary:
>retro_ptro_688
ATGGAGGGGGTGCTGTACAAGTGGACCAACTATCTGAGCGGTTGGCAGCCTTGATGGTTCCTTCTCTGTGGGGGAATATT
GTCCTATTATGATTCTCCTGAAGATGCCTGGAAAGGTTGAAAAGGGAGCATACAAATGGCAGTCTGTGAAATTGAAGTTC
ATTCTGTAGATAATACATGCATGCACCTGATAATCCCCGGGGAACAGTATTTCTACCTGAAGGCCAGAAGTGTGCCTGAA
AGATAGCGGCAGCTGGTGGCCCTGGGATCAGCCGAGGCTTGCCTGACTGACAGTAGGACCCAGAAGGATAAAGAGTTTGC
TGAAAACACTGAAAACTTGAAAACCAAAATGTCAGAACTAAGACTCTGCTGTGACCTCCTTGTTCAGCAAGTAGATAAAA
CAAAAGAAGTGACCACAACTGGTGTGTCCAATTCTGAGGAGGGAATTGATGTGGGAATCAATGCTGAAATCAACCTGTAA
TACTTTTCTGAAGACCTTGGAAGAATGCATGCAGATTGCAAATGCAGCCTTCACCTCTGAGCTGCTCTACCACACTCCAC
CAGGATCACCACAGCTGGCCATGCTCAAGTCCAGCAAGATGAAACATCCTATTATACCAATTCATAATTCATTGGAAAGG
CAAATGGAGTTGAGCACTTGTGAAAATGGATCTTTAAATATGGAAATAAATGGTGAGGAAGAAATCCTAATGAAAAATAA
GAATTCCTTATATTTGAAATCTGCAGAGATAGACTGCAGCATATCAAGTGAGGAAAATACAGATGATAATATAACCGTCC
AAGGTGAAATAATGAAGGAAGATGGAATGGAAAACCTGAAAAATCATGACAATAACTTGTCTCAGTCTGGATCAGACTCA
AGTTGCTCTCCAGAATGCCTCTGGGAGGAAGGCAAAGAAGTTATCCCAACTTTCTTTAGTACCATGAACACAAGCTTTAG
TGACATTGAACTTCTGGAAGACAGTGGCATTCCCACAGAAGCATTCTTGGCATCATGTTGTGCTGTGGTTCCAGTATTAG
ACAAACTTGGCCCTACAGTGTTTGCTCCTGTTAAGATGGATCTTGTTGGAAATATTAAGAAAGTAAATCAGAAGTATATA
ACCAACAAAGAAGAGTTTACCACTCTCCAGAAGATAGTTCTGCACGAAGTGGAGGCGGATGTAGCCCAGGTTAGGAACTC
AGCGACTGAAGCCCTCTTGTGGCTGAAGAGAGGTCTCCAATTTTTTAAGGGATTTTTGACAGAAGTGAAAAATGGGGAAA
AGGATATCCAGACAGCCCTGAATAACGCATATGGTAAAACATTGCGGCAACACCATGGCTGGGTAGTTCGAGGGGTTTTT
GCGTTAGCTTTAAGGACAACTCCATCCTATGAAGATTTTGTGGCCGCGTTAACCATAAAGGAAGGTGACCACCAGAAAGA
AGCTTTCAGTATTGGGATGCAGAGGGACCTCAGCCTTTACCTCCCTGCCATGGAGAAGCAGATGGCCATACTGGACGCTT
TATAAGAGGTCCATGGGCTGGAATCTGATGAGGTGGTA
ORF - retro_ptro_688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MEGVLYKWTNYLSGWQPRWFLLCGGILSYYDSPEDAWKGCKGSIQMAVCEIQVHSVDNTRMDLIIPGEQY |
| MEGVLYKWTNYLSGWQP.WFLLCGGILSYYDSPEDAWKG.KGSIQMAVCEI.VHSVDNT.M.LIIPGEQY | |
| Retrocopy | MEGVLYKWTNYLSGWQP*WFLLCGGILSYYDSPEDAWKG*KGSIQMAVCEIEVHSVDNTCMHLIIPGEQY |
| Parental | FYLKARSVAERQRWLVALGSAKACLTDSRTQKEKEFAENTENLKTKMSELRLYCDLLVQQVDKTKEVTTT |
| FYLKARSV.ER.R.LVALGSA.ACLTDSRTQK.KEFAENTENLKTKMSELRL.CDLLVQQVDKTKEVTTT | |
| Retrocopy | FYLKARSVPER*RQLVALGSAEACLTDSRTQKDKEFAENTENLKTKMSELRLCCDLLVQQVDKTKEVTTT |
| Parental | GVSNSEEGIDVG-TLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIHN |
| GVSNSEEGIDVG...LKSTCNTFLKTLEECMQIANAAFTSELLY.TPPGSPQLAMLKSSKMKHPIIPIHN | |
| Retrocopy | GVSNSEEGIDVG>SMLKSTCNTFLKTLEECMQIANAAFTSELLYHTPPGSPQLAMLKSSKMKHPIIPIHN |
| Parental | SLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEIRKEDGLENL |
| SLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEI.KEDG.ENL | |
| Retrocopy | SLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEIMKEDGMENL |
| Parental | KNHDNNLTQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCYAVVPVLDKL |
| KNHDNNL.QSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASC.AVVPVLDKL | |
| Retrocopy | KNHDNNLSQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCCAVVPVLDKL |
| Parental | GPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLKFLKGFL |
| GPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGL.F.KGFL | |
| Retrocopy | GPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLQFFKGFL |
| Parental | TEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRAAPSYEDFVAALTVKEGDHQKEAFSIGMQRD |
| TEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALR..PSYEDFVAALT.KEGDHQKEAFSIGMQRD | |
| Retrocopy | TEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRTTPSYEDFVAALTIKEGDHQKEAFSIGMQRD |
| Parental | LSLYLPAMEKQLAILDTLYEVHGLESDEVV |
| LSLYLPAMEKQ.AILD.L.EVHGLESDEVV | |
| Retrocopy | LSLYLPAMEKQMAILDAL*EVHGLESDEVV |
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 .11 RPM | 12 .96 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 23 .98 RPM |
| SRP007412_heart | 0 .17 RPM | 6 .41 RPM |
| SRP007412_kidney | 0 .08 RPM | 24 .84 RPM |
| SRP007412_liver | 0 .07 RPM | 7 .27 RPM |
| SRP007412_testis | 0 .00 RPM | 11 .17 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_688 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_688 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_688 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1110 |
| Pongo abelii | retro_pabe_919 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000106086 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000006031 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017682 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000005431 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000019036 | 1 retrocopy |
retro_ptro_688 ,
|