RetrogeneDB ID: | retro_tbel_4240 | ||
Retrocopy location | Organism: | Treeshrew (Tupaia belangeri) | |
| Coordinates: | scaffold_72901:19870..20992(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GFAP | ||
| Ensembl ID: | ENSTBEG00000011873 | ||
| Aliases: | None | ||
| Description: | glial fibrillary acidic protein [Source:HGNC Symbol;Acc:4235] |
Retrocopy-Parental alignment summary:
>retro_tbel_4240
CTGCAGGCCTCAGTGGACTTCTCGCTGGCTGACGCCATCAACACCGAGTTCAAGAACACTCACACCAATGAGAAAGTGGA
GCTGCAGGAACTGAATGACTGATTCGCCAACTACATCGACAAGGTGTGCTTCTTGGAGCAGCAGAACAAGATCCTGATGG
CCGAGCTCAAGCAGCTCAAGGGCCAGAGCAAGTCGTGCCTGGGGGACCTCTATGAGGAGGAGATGCGGGAGCTGCACAGG
CAGGTGGATAAGCTCACCAACGAGAAGGCCCACGTGGAGGTGGAGCGTGACAACCTGGCCAAGGACATCATGAGGCTTTG
GGAGAAATTGCAGGAGGAGATGCTTCAGAGAGAGGAAGCTGAAAGCACTCTGCAATCTTTCAGACAGGATGTTGACAATG
CTTCTTTGGCACGTCTTGACCTTGAGCACAAAGTGGAGTCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACACAAA
GAGGAAATTCAGTAGCTGCAAGCCCAGATTCAGGAACAGCATGTCCAAGTTGATATGGATGTTTCCAAGACTGACCTCAC
GGCTGCCCTGCATGATGTCTGTCAGCAGTATGAAAGTGTAGCTGCCAAGAACCTTCAGGAGGCAGAAGAATGGTACAAGT
CCAAGTTTGCTGACCTCTCAGAAGCTGCTAACCACAACAACGATGCCCTGTGCCAGGCGAAGCAGGAGTCCAATGAGTAC
TGGCGGCAGGTGCAGTCCCTCACCTATGAAGTGGATGTGCTTAAAGGAACTAATGAATCTCTGGAATGCCAGATGTGTGA
AATGGCAGAGAACTTTGCTGTCGAAGCTGCTAACTACCAAGACACCACTGGCCACCTGCAGGATGAGATTCAGAACATGA
AGGAAGAAATGGCTCGCCACCTTCGTGAATACCAGGACCTGCTCAATGTTAAGATGGCTCTTGACATTGAGATTGCCACC
TACAGGAAGCTGCTGGAAGGCGAGGAAAGCAGGATTTCTCTGCCTCTTCCAAACTTCTCCTCCCTGAATCTGAGGGACAC
TAATCTGGATTCACTCCCTCTGGTTGACACCCACCCAAAAAGAACACTTCTGATTAAGACGGTTAAAACTAGTGATGGAC
AG
ORF - retro_tbel_4240 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.15 % |
| Parental protein coverage: | 90.34 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LPARVDFSLAGALNAGFKETRASERAEMMELNDRFASYIEKVRFLEQQNKALAAELNQLRAKEPTKLADV |
| L.A.VDFSLA.A.N..FK.T...E..E..ELND.FA.YI.KV.FLEQQNK.L.AEL.QL.......L.D. | |
| Retrocopy | LQASVDFSLADAINTEFKNTHTNEKVELQELND*FANYIDKVCFLEQQNKILMAELKQLKGQSKSCLGDL |
| Parental | YQAELRELRLRLDQLTANSARLEVERDNLAQDLTTLRQKLQDETNLRMEAENNLAAYRQEADEATLARLD |
| Y..E.REL....D.LT...A..EVERDNLA.D...L..KLQ.E...R.EAE..L...RQ..D.A.LARLD | |
| Retrocopy | YEEEMRELHRQVDKLTNEKAHVEVERDNLAKDIMRLWEKLQEEMLQREEAESTLQSFRQDVDNASLARLD |
| Parental | LERKTESLEEEIQFLRKIHEEEVRELQEQLARQQVHVELDVAKPDLTAALREIRTQYEAMASSNMHEAEE |
| LE.K.ESL.EEI.FL.K.H.EE...LQ.Q...Q.V.V..DV.K.DLTAAL.....QYE..A..N..EAEE | |
| Retrocopy | LEHKVESLQEEIAFLKKLHKEEIQ*LQAQIQEQHVQVDMDVSKTDLTAALHDVCQQYESVAAKNLQEAEE |
| Parental | WYRSKFADLTDAAARNAELLRQAKHEANDYRRQLQALTCDLESLRGTNESLERQMREQEERHAREAASYQ |
| WY.SKFADL..AA..N...L.QAK.E.N.Y.RQ.Q.LT.....L.GTNESLE.QM.E..E..A.EAA.YQ | |
| Retrocopy | WYKSKFADLSEAANHNNDALCQAKQESNEYWRQVQSLTYEVDVLKGTNESLECQMCEMAENFAVEAANYQ |
| Parental | EALARLEEEGQSLKDEMARHLQEYQELLNVKLALDIEIATYRKLLEGEENRITIPVQTFSNLQIRETSLD |
| .....L..E.Q..K.EMARHL.EYQ.LLNVK.ALDIEIATYRKLLEGEE.RI..P...FS.L..R.T.LD | |
| Retrocopy | DTTGHLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSSLNLRDTNLD |
| Parental | TKSVSEGHLKRNIVVKTVEMRDGE |
| .......H.KR....KTV...DG. | |
| Retrocopy | SLPLVDTHPKRTLLIKTVKTSDGQ |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Tupaia belangeri was not studied using RNA-Seq expression data.
Tupaia belangeri was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_tbel_4240 retrocopy.
Tupaia belangeri was not studied using FANTOM5 data.
retro_tbel_4240 was not experimentally validated.
Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Tupaia belangeri | ENSTBEG00000011873 | 2 retrocopies |
retro_tbel_4240 , retro_tbel_4726,
|
| Tupaia belangeri | ENSTBEG00000014942 | 1 retrocopy |