RetrogeneDB ID: | retro_ptro_106 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | Y:20698081..20698939(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSPTRG00000006940 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM92B | ||
| Ensembl ID: | ENSPTRG00000008427 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 92, member B [Source:HGNC Symbol;Acc:24781] |
Retrocopy-Parental alignment summary:
>retro_ptro_106
CGGGAGACGCTGGGTCGGAACGCTCAAACGAAACAACTGCAAACAGCTGTCTCAAATGTGGAGAAGCATTTTGGAGAACT
GTGCCAAATCTTCGCTGCCTATGTGCGGAAAACTGCCAGGCTGAGAGACAAAGCAGACCTCCTGGTGAATGAAATTAACG
CGTATGCTGCTACAGAGACCCCGCATTTAAAGCTGGGCCTGATGAACTTTGCAGATGAGTTTGCCAAACTTCAGGATTAT
CGACAAGCAGAGGTTGAAAGACTTGAAGCCAAAGTAGTTGAACCCTTGAAAACTTATGGGACCATTGTGAAAATGAAACG
GGATGACCTCAAAGCAACACTCACAGCAAGGAATCGAGAAGCTAAGCAATTAACTCAGTTAGAAAGAACACGTCAGCGAA
ACCCATCTGATCGACATGTTATTTCACAGGCAGAAACGGAATTACAGAGAGCTGCAATGGATGCTAGCCGAACAAGTCGT
CATCTGGAGGAAACTATTAACAACGTTGAAACGCAGAAAATGAAGGATATAAAGACTATATTTTCTGAATTTATCACAAT
CGAAATGTTATTTCACGGCAAAGCTTTAGAGGTCTACACTGCTGCCTACCAGAATATACAAAACATTGACGAAGATGAAG
ATTTAGAGGTTTTCCGAAATTCTCTGTATGCACCAGATCATTCATCTCGTTTAGATATTGTAAGAGCAAATTCAAAGTCA
CCTCTTCAGAGATCACTGTCAGCTAAGTGTGTATCTGGAACAGGACAGGTATCCACTTGTCGACTAAGAAAGGATCAACA
AGCAGAAGATGATGAGGATGAAGAGTTAGATGTTACAGAAGAAGAAAATTTTCTTAAG
ORF - retro_ptro_106 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.93 % |
| Parental protein coverage: | 70.39 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RDSQVRVMENIVANTEKYFGQFCSLLAAYTRKTARLRDKADQLVKQLIDFANSENPELRATMRGFAEDLA |
| R..Q.......V.N.EK.FG..C...AAY.RKTARLRDKAD.LV......A..E.P.L......FA...A | |
| Retrocopy | RNAQTKQLQTAVSNVEKHFGELCQIFAAYVRKTARLRDKADLLVNEINAYAATETPHLKLGLMNFADEFA |
| Parental | KVQDYRQAQVERLETKVVNPLKLYGAQIKQTRAEIKKFKHVQNHEIKQLEKLEKLRQKSPSDQQMIGQAE |
| K.QDYRQA.VERLE.KVV.PLK.YG...K..R...K......N.E.KQL..LE..RQ..PSD...I.QAE | |
| Retrocopy | KLQDYRQAEVERLEAKVVEPLKTYGTIVKMKRDDLKATLTARNREAKQLTQLERTRQRNPSDRHVISQAE |
| Parental | TRVQRAAVDSSRTTLHLEETVDAFQRQKLKDLQKFFCDFVTIEMVFHAKAVEVYSSAFQTLEKYDLERDL |
| T..QRAA.D.SRT..HLEET......QK.KD....F..F.TIEM.FH.KA.EVY..A.Q.....D...DL | |
| Retrocopy | TELQRAAMDASRTSRHLEETINNVETQKMKDIKTIFSEFITIEMLFHGKALEVYTAAYQNIQNIDEDEDL |
| Parental | LDFR |
| ..FR | |
| Retrocopy | EVFR |
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 | 5 .63 RPM | 0 .02 RPM |
| SRP007412_cerebellum | 3 .87 RPM | 0 .22 RPM |
| SRP007412_heart | 4 .93 RPM | 0 .00 RPM |
| SRP007412_kidney | 3 .98 RPM | 0 .00 RPM |
| SRP007412_liver | 2 .55 RPM | 0 .00 RPM |
| SRP007412_testis | 70 .50 RPM | 0 .00 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
1 EST(s) were mapped to retro_ptro_106 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| EX654481 | 38071171 | 38071276 | 95.3 | 100 | 5 | 95 |
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_106 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_106 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pan troglodytes | ENSPTRG00000008427 | 1 retrocopy |
retro_ptro_106 ,
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