General information for g2872.t3
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.t3 | isoform | g2872.t3 | 20820467 | 20829511 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon1 | 20820467 | 20820738 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS1 | 20820571 | 20820738 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon2 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS2 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon3 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS3 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon4 | 20821144 | 20821620 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS4 | 20821144 | 20821620 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon5 | 20821678 | 20821731 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS5 | 20821678 | 20821731 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon6 | 20822490 | 20822781 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS6 | 20822490 | 20822781 |
| chr_3 | g2872 | g2872.t3 | exon | g2872.t3.exon7 | 20829346 | 20829511 |
| chr_3 | g2872 | g2872.t3 | cds | g2872.t3.CDS7 | 20829346 | 20829404 |
| chr_3 | g2872 | g2872.t3 | TSS | g2872.t3 | 20829511 | 20829511 |
| chr_3 | g2872 | g2872.t3 | TTS | g2872.t3 | NA | NA |
Sequences
>g2872.t3 Gene=g2872 Length=1477
AGTTTGAGGTTTAACTTTATCAAGATAAGACGTGTTTTATAATTTCTCTTTACGTAAATT
AACATGAAATAAAACTCTAATTATTTATTTGCCAAGTGTATGTGTAGATGTCAGATCTTT
ATAATTGTTCTAGAGTCATTTTTAAAGTATTAGTGTCCACAATATCATGGCGAGGATCAA
TTTATAAATTACTTTGGCTTGACTTAACATCATTTCTCTTAATATACTACACATTAAATC
TAACTTACCGCCTTGCACTTAATGAAGATCAGAAAAAAACATTTGAAGCTTTAGTAAAAT
ATTGCGATGAACATTCCAATCTTATTCCACTATCATTTGTCCTCGGTTTTTATGTGTCGA
TAGTCATGACTAGATGGTGGAATCAATACACTTCAATTCCGTGGCCAGATCCAATTGCAG
TCTTTGTAAGTGCAACCGTTCATGGTCAGGACGAGCGAGGTAGAGTGATGCGCAGAACAA
TTATGCGATATGTATGTTTGTGCATAAGTATGGTACTTGGAAACTTATCACCTAAAGTGA
AAAAACGTTTTCCAACTTTAAATCATTACGTCGAAGCAGGTCTTTTGAACGAAAATGAAC
GAGATATTATTGAAGATTTAAATAATAAATTTCCTCGTCATTCCAAGCATTGGTTGCCAA
TAGTATGGGCTGCAAGTATAATCACTAGAGCTCGCAAGGAAGGACGAATTCGTGATGATT
TTGCTGTCAAGACAATTATCGATGAATTAAATAAATTTCGTGGACAATGTGGAGTGTTAA
TCGCCTATGACACTATTTCCATACCATTGGTTTACACTCAAGTTGTGACTATAGCTGTTT
ACTCTTACTTTTTGGTAGCTCTATTAGGACAGCAATGGACAGAAGGGAAAGGAACGGAAA
ATGGATATCAAAATCGATTTGATTTATACTTTCCAGTATTCAGTCTTTTACAATTTTTTT
TCTATATGGGATGGCTTAAAGTGGCAGAGCAACTTATAAATCCTTTCGGCGAAGATGACG
ATGATTTTGAAGTAAATTGGATGATTGATAGAAACCTGCAGGTCAGCTATTTAATTGTAG
ATGATATTCATAATAGTCATCCAGAACTCATTAAAGATCAATATTGGGATAGTATTCTTG
TACAAGATTTGCCATATACAGTTGCTTCAATGGGAAATCGAGAAAATCCACCAGAACCTT
CAACAGCAAATGTAGAGGTCAAAAAGGGTGGAGCTGAAATTGTGACCGCACCATCAGTGG
CTAAAAACATGGATGATATGGTCGGTAAAAATACTGCAACTACAAATTATGAGTTTCCCG
ATAATGATAATGACAGTGATAAGGTTAGCCGCGTTTCAAAATTCTTCAAATGATCTCAAA
ATTTTCTAAAGTTTCTATCACATTCTCTATCTAATCATATGTACAATAAAAAATTTAAAA
TTTCTTTTATTCTCATTTTATTCCAAATTGGTGAAGG
>g2872.t3 Gene=g2872 Length=421
MSDLYNCSRVIFKVLVSTISWRGSIYKLLWLDLTSFLLIYYTLNLTYRLALNEDQKKTFE
ALVKYCDEHSNLIPLSFVLGFYVSIVMTRWWNQYTSIPWPDPIAVFVSATVHGQDERGRV
MRRTIMRYVCLCISMVLGNLSPKVKKRFPTLNHYVEAGLLNENERDIIEDLNNKFPRHSK
HWLPIVWAASIITRARKEGRIRDDFAVKTIIDELNKFRGQCGVLIAYDTISIPLVYTQVV
TIAVYSYFLVALLGQQWTEGKGTENGYQNRFDLYFPVFSLLQFFFYMGWLKVAEQLINPF
GEDDDDFEVNWMIDRNLQVSYLIVDDIHNSHPELIKDQYWDSILVQDLPYTVASMGNREN
PPEPSTANVEVKKGGAEIVTAPSVAKNMDDMVGKNTATTNYEFPDNDNDSDKVSRVSKFF
K
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2872.t3 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 18 | 390 | 2.2E-201 |
| 3 | g2872.t3 | PANTHER | PTHR10736 | BESTROPHIN | 18 | 390 | 2.2E-201 |
| 1 | g2872.t3 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 18 | 318 | 3.6E-92 |
| 11 | g2872.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 27 | - |
| 17 | g2872.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 51 | - |
| 10 | g2872.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 52 | 71 | - |
| 18 | g2872.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 91 | - |
| 13 | g2872.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 92 | 124 | - |
| 16 | g2872.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 142 | - |
| 9 | g2872.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 143 | 233 | - |
| 15 | g2872.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 253 | - |
| 12 | g2872.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 254 | 272 | - |
| 14 | g2872.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 290 | - |
| 8 | g2872.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 291 | 421 | - |
| 5 | g2872.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 51 | - |
| 7 | g2872.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 91 | - |
| 6 | g2872.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 230 | 252 | - |
| 4 | g2872.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 290 | - |
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 K13879 (bestrophin-2)
Pathway
- This transcript belongs to the following 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.
