General information for g2872.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bestrophin-2.
Parent gene
- The parent gene g2872 is located on chr_3: 20822582..20829511 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2872 | g2872.t1 | TTS | g2872.t1 | 20818713 | 20818713 |
| chr_3 | g2872 | g2872.t1 | isoform | g2872.t1 | 20819156 | 20822582 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon1 | 20819156 | 20819259 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS1 | 20819156 | 20819259 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon2 | 20819318 | 20820068 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS2 | 20819318 | 20820068 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon3 | 20820396 | 20820467 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS3 | 20820396 | 20820467 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon4 | 20820601 | 20820738 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS4 | 20820601 | 20820738 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon5 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS5 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon6 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS6 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon7 | 20821144 | 20821620 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS7 | 20821144 | 20821620 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon8 | 20821678 | 20821731 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS8 | 20821678 | 20821731 |
| chr_3 | g2872 | g2872.t1 | exon | g2872.t1.exon9 | 20822490 | 20822582 |
| chr_3 | g2872 | g2872.t1 | cds | g2872.t1.CDS9 | 20822490 | 20822582 |
| chr_3 | g2872 | g2872.t1 | TSS | g2872.t1 | NA | NA |
Sequences
>g2872.t1 Gene=g2872 Length=1905
ATGACTAGATGGTGGAATCAATACACTTCAATTCCGTGGCCAGATCCAATTGCAGTCTTT
GTAAGTGCAACCGTTCATGGTCAGGACGAGCGAGGTAGAGTGATGCGCAGAACAATTATG
CGATATGTATGTTTGTGCATAAGTATGGTACTTGGAAACTTATCACCTAAAGTGAAAAAA
CGTTTTCCAACTTTAAATCATTACGTCGAAGCAGGTCTTTTGAACGAAAATGAACGAGAT
ATTATTGAAGATTTAAATAATAAATTTCCTCGTCATTCCAAGCATTGGTTGCCAATAGTA
TGGGCTGCAAGTATAATCACTAGAGCTCGCAAGGAAGGACGAATTCGTGATGATTTTGCT
GTCAAGACAATTATCGATGAATTAAATAAATTTCGTGGACAATGTGGAGTGTTAATCGCC
TATGACACTATTTCCATACCATTGGTTTACACTCAAGTTGTGACTATAGCTGTTTACTCT
TACTTTTTGGTAGCTCTATTAGGACAGCAATGGACAGAAGGGAAAGGAACGGAAAATGGA
TATCAAAATCGATTTGATTTATACTTTCCAGTATTCAGTCTTTTACAATTTTTTTTCTAT
ATGGGATGGCTTAAAGTGGCAGAGCAACTTATAAATCCTTTCGGCGAAGATGACGATGAT
TTTGAAGTAAATTGGATGATTGATAGAAACCTGCAGGTCAGCTATTTAATTGTAGATGAT
ATTCATAATAGTCATCCAGAACTCATTAAAGATCAATATTGGGATAGTATTCTTGTACAA
GATTTGCCATATACAGTTGCTTCAATGGGAAATCGAGAAAATCCACCAGAACCTTCAACA
GCAAATGTAGAGGTCAAAAAGGGTGGAGCTGAAATTGTGACCGCACCATCAGTGGCTAAA
AACATGGATGATATGGTCGGTAAAAATACTGCAACTACAAATTATGAGTTTCCCGATAAT
GATAATGACAGTGATAAGGAAAAAATGCTAAAAATACCATGCACAGTACACACAACAAAA
TCAGGCTTGTTTGCGACACAGCTATCCAATGACAACGATGATAATGCTAGTGGTATTCAT
TTTACTGCGAGTGGCAGACGAAGAAATACAAGTGGATCAGCTTCAGCTACATCTATGCAT
TCACTTGCTGGTACAATGAGTCGTGTTAATACAGTGACTTCATTATTGAAACGCTTCTTG
AGTAAAGACGATAGCAGAGGTGAAAGTAGACCTGGAAGCGCGGCAGCAAATAGTAGTGCA
GAAAAAGGTTTAGGAACATCAGCTAGTTCAGCAAGTATCGTTGGCAAACAACATCCAAAT
CAAATAGGCAGCATGAAAATCACAGATCAAGTTATTGAAGAAGTTGACGAGCAAATGACA
ATAAATTCACTTCGAAACAAAGAAGATCCTCGTCCAACAGCACAAAGTCTTTTTATTAAT
AATCCAATTGCAGCTGGAAGTAGTGCACCAATCGATGTTCCTGGTACTGTAACTCATCCT
CATCATTATGGAAGATTTTATTCAGCACAAGTTACAGATGATGATATGTTCCCTCCTGAT
GATCTCATGAGTTCATCTGCACCAGTTGGAAAACCTTCAGCAACTAGTTCACAACATCCA
ACTTTAATATCAGAGTTTGACCCTAAACCTTTTGTAGAAGATAATGCTAAAACAGAAAAT
ATTGAAGAACACGATAGCACAAAGCCTGACGATGAGTTTGAACTTTTAAGGCAGCAACGT
GAAGCAGATCGAATTGCTAGACAAAAGGAGAAAATTGCTAGAAGTATATCAGCACAGCAA
GGAGTAGTTAACCAAATTGAATTGCAAGATTTACTTAATAATGCTTTAGCATCAAATGTA
GCACAATCTGAAAGTGGAAACAGCAGTCCAACACTCGAAGGTTAA
>g2872.t1 Gene=g2872 Length=634
MTRWWNQYTSIPWPDPIAVFVSATVHGQDERGRVMRRTIMRYVCLCISMVLGNLSPKVKK
RFPTLNHYVEAGLLNENERDIIEDLNNKFPRHSKHWLPIVWAASIITRARKEGRIRDDFA
VKTIIDELNKFRGQCGVLIAYDTISIPLVYTQVVTIAVYSYFLVALLGQQWTEGKGTENG
YQNRFDLYFPVFSLLQFFFYMGWLKVAEQLINPFGEDDDDFEVNWMIDRNLQVSYLIVDD
IHNSHPELIKDQYWDSILVQDLPYTVASMGNRENPPEPSTANVEVKKGGAEIVTAPSVAK
NMDDMVGKNTATTNYEFPDNDNDSDKEKMLKIPCTVHTTKSGLFATQLSNDNDDNASGIH
FTASGRRRNTSGSASATSMHSLAGTMSRVNTVTSLLKRFLSKDDSRGESRPGSAAANSSA
EKGLGTSASSASIVGKQHPNQIGSMKITDQVIEEVDEQMTINSLRNKEDPRPTAQSLFIN
NPIAAGSSAPIDVPGTVTHPHHYGRFYSAQVTDDDMFPPDDLMSSSAPVGKPSATSSQHP
TLISEFDPKPFVEDNAKTENIEEHDSTKPDDEFELLRQQREADRIARQKEKIARSISAQQ
GVVNQIELQDLLNNALASNVAQSESGNSSPTLEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 361 | 382 | - |
| 11 | g2872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 402 | 444 | - |
| 8 | g2872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 411 | 444 | - |
| 10 | g2872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 524 | 543 | - |
| 9 | g2872.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 528 | 543 | - |
| 2 | g2872.t1 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 1 | 479 | 9.7E-173 |
| 3 | g2872.t1 | PANTHER | PTHR10736 | BESTROPHIN | 1 | 479 | 9.7E-173 |
| 1 | g2872.t1 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 1 | 232 | 3.1E-72 |
| 13 | g2872.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 38 | - |
| 17 | g2872.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 56 | - |
| 14 | g2872.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 57 | 147 | - |
| 18 | g2872.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 148 | 167 | - |
| 12 | g2872.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 168 | 186 | - |
| 16 | g2872.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 204 | - |
| 15 | g2872.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 205 | 634 | - |
| 5 | g2872.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 56 | - |
| 6 | g2872.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 144 | 166 | - |
| 4 | g2872.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 204 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K22204 (bestrophin, other)
Pathway
This gene does not belong to any pathways.
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
