RetrogeneDB ID: | retro_pabe_919 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:44677749..44679297(-) | ||
| 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: | ENSPPYG00000017682 | ||
| Aliases: | None | ||
| Description: | pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 [Source:HGNC Symbol;Acc:30037] |
Retrocopy-Parental alignment summary:
>retro_pabe_919
ATGGAGGGGGTGCTGTACAAGTGGCCAAACTATCTGAGCAGTTGGCAGCCTCGATGGTTCCTTCTCTGTGGGGGAATATT
GTCCTATTATGATTCTCCTGAAGATGCCTGAAAAGGTTGCAAAGGGAGCATACAAATGGCAGTCTGTGAAATTCAACTTC
ATTCTGTAGATAATACATGCGTGGACCTGATAATCCCCAGGGAACAGTATTTCTACCTGAAGTCCAGAAGTGTGGCTGAA
AGATAGCAGTGGCTGGTGGCCCTGGGATCAGCCAAGGCTTGCCTGACTGACAGTAGGACCCAGAAGGAGAAAGAGTTTGC
TGAAAACTTGAAAACCAAAATGTCAGAATTAAGACTCTGCTGTGACCTCCTTGTTCAGCAAGTAGATAAAACAAAAGAAG
TGACCACAACTGGTGTGTCCAATTCTGAGGAGGGAATTGATGTGGGAACTTTGCTGAAATCAACCTGTAATACTTTTCTG
AAGACCTTGGAAGAATGCATGCAGATCGCAAATGCAGCCTTCACCTCCGAGCTGCTCTACCGCACTCCACCAGGATCACC
GCAGCTGGCCATGCTCAAGTCCAGCAAGATGAAACATCCTATTATACCAATTCGTAATTCATTGGAAAGGCAAATGGAGT
TGAGCACTTGTGAAAATGGATCTTTAAATATGGAAATAAATGGTGAGGAAGAAATCCTAATGAAAAATAAGAATTCCTTT
TATTTGAAATCTGCAGAGATAGACTGCAGCACATCAAGTGAGGAAAATACAGATGATAATGTAACAGTCCAAGGTGAAAT
AATGAAGGAAGATGGAATGGAAAACCTGAAAAATCTTGACAGTAACTCGACTCAGTCTGGATCAGACTCAAGTTGCTCTC
CAGAATGCCTCTGGGAGGAAGGCAAAGAAGTTATCCCAACTTTCTTTAGTACCATGAACACAAGCTTTAGTGACATTGAA
CTTCTGGAAGACAGTGGCATTCCCGCAGAAGCATTCTTGGCATCATGCTATGCTGTGGTTCCAGTATTAGACAAACTTGG
CCCTACAGTGTTTGCTCCTGTTAAGATGGATCTTGTTGGAAATATTAAGAAAGTAAATCAGAAGTATATAACCAACAAAG
AAGAGTTTACCACTCTCCAGAAGATAGTGCTGCACGAAGTGGAGGTGGATGTAGCCCAGGTTAGGAACTCAGCGACTGAA
GCCCTCTTGTGGCTGAAGAGAGGTCTCAAATTTTTGAAGGGATTTTTGACAGAAGTGAAAAATGGGGAAAAGGATATCCA
GACAGCCCTGAATAACGCATATGGTAAAACATTGCGGCAACACAATGGCTGGGTATTTCGAGTGGTTTTTGCGTTAGCTT
TAAGGTCAACTCTATCCTATGAAGATTTTGTGGCTGTGTTAACCATAAAGGAAGGTGACCACCAGAAAGAAGCTTTCAGT
ATTGGGATGCAGAGGGACCTCAGCCTTTACCTCCCTGCCATGGAGAAGCAGCTGGCCATACTGGACGCTTTAGAAGAGGT
CCACAGGCTGGAATCTGATGAGGTGGTA
ORF - retro_pabe_919 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.87 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MEGVLYKWTNYLSGWQPRWFLLCGGILSYYDSPEDAWKGCKGSIQMAVCEIQVHSVDNTRMDLIIPGEQY |
| MEGVLYKW.NYLS.WQPRWFLLCGGILSYYDSPEDA.KGCKGSIQMAVCEIQ.HSVDNT..DLIIP.EQY | |
| Retrocopy | MEGVLYKWPNYLSSWQPRWFLLCGGILSYYDSPEDA*KGCKGSIQMAVCEIQLHSVDNTCVDLIIPREQY |
| Parental | FYLKARSVAERQRWLVALGSAKACLTDSRTQKEKEFAENTENLKTKMSELRLYCDLLVQQVDKTKEVTTT |
| FYLK.RSVAER..WLVALGSAKACLTDSRTQKEKEFA...ENLKTKMSELRL.CDLLVQQVDKTKEVTTT | |
| Retrocopy | FYLKSRSVAER*QWLVALGSAKACLTDSRTQKEKEFA---ENLKTKMSELRLCCDLLVQQVDKTKEVTTT |
| Parental | GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIHNS |
| GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPI.NS | |
| Retrocopy | GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIRNS |
| Parental | LERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEVMKEDGMENLK |
| LERQMELSTCENGSLNMEINGEEEILMKNKNS.YLKSAEIDCS.SSEENTDDN.TVQGE.MKEDGMENLK | |
| Retrocopy | LERQMELSTCENGSLNMEINGEEEILMKNKNSFYLKSAEIDCSTSSEENTDDNVTVQGEIMKEDGMENLK |
| Parental | NHDNNLTQSGSDSSCSPEFLWEESKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCYAVVPVLDKLG |
| N.D.N.TQSGSDSSCSPE.LWEE.KEVIPTFFSTMNTSFSDIELLEDSGIP.EAFLASCYAVVPVLDKLG | |
| Retrocopy | NLDSNSTQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPAEAFLASCYAVVPVLDKLG |
| Parental | PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLKFLKGFLT |
| PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVE.DVAQVRNSATEALLWLKRGLKFLKGFLT | |
| Retrocopy | PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEVDVAQVRNSATEALLWLKRGLKFLKGFLT |
| Parental | EVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRAAPSYEDFVAALTIKEGDHQKEAFSTGMQRDL |
| EVKNGEKDIQTALNNAYGKTLRQH.GWV.R.VFALALR...SYEDFVA.LTIKEGDHQKEAFS.GMQRDL | |
| Retrocopy | EVKNGEKDIQTALNNAYGKTLRQHNGWVFRVVFALALRSTLSYEDFVAVLTIKEGDHQKEAFSIGMQRDL |
| Parental | SLYLPAMEKQLAILDTLYEVHGLESDEVV |
| SLYLPAMEKQLAILD.L.EVH.LESDEVV | |
| Retrocopy | SLYLPAMEKQLAILDALEEVHRLESDEVV |
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 .39 RPM | 2 .76 RPM |
| SRP007412_cerebellum | 0 .61 RPM | 4 .74 RPM |
| SRP007412_heart | 1 .81 RPM | 1 .08 RPM |
| SRP007412_kidney | 2 .09 RPM | 5 .10 RPM |
| SRP007412_liver | 1 .77 RPM | 4 .25 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_919 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_919 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_919 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1110 |
| Pan troglodytes | retro_ptro_688 |
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 | ENSPPYG00000004939 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017682 | 1 retrocopy |
retro_pabe_919 ,
|
| Pan troglodytes | ENSPTRG00000019036 | 1 retrocopy |