General information for g114.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bestrophin-2.
Parent gene
- The parent gene g114 is located on chr_3: 990685..992508 (- 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 | g114 | g114.t1 | isoform | g114.t1 | 990685 | 992508 |
| chr_3 | g114 | g114.t1 | exon | g114.t1.exon1 | 990685 | 991334 |
| chr_3 | g114 | g114.t1 | cds | g114.t1.CDS1 | 990685 | 991334 |
| chr_3 | g114 | g114.t1 | exon | g114.t1.exon2 | 991392 | 991553 |
| chr_3 | g114 | g114.t1 | cds | g114.t1.CDS2 | 991392 | 991553 |
| chr_3 | g114 | g114.t1 | exon | g114.t1.exon3 | 991612 | 991884 |
| chr_3 | g114 | g114.t1 | cds | g114.t1.CDS3 | 991612 | 991884 |
| chr_3 | g114 | g114.t1 | exon | g114.t1.exon4 | 992241 | 992508 |
| chr_3 | g114 | g114.t1 | cds | g114.t1.CDS4 | 992241 | 992508 |
| chr_3 | g114 | g114.t1 | TSS | g114.t1 | NA | NA |
| chr_3 | g114 | g114.t1 | TTS | g114.t1 | NA | NA |
Sequences
>g114.t1 Gene=g114 Length=1353
ATGACTGTGAGTTATGCAGAAGATTTGTTATCAGCAAGTGGAATGTCTTTAATCAAATTG
GTATTTTTAAAATGGAAAGGATCATTGTTTAAACTTATTTGGAAAGATTTGTTGATGTTT
ATCTCAATGTTTTACATTCTACAAGGAATTTATGTTTTTGGTATCTCAGAAGAAAATAAA
AAATATTTTGAAGGTTTGGTGTATTATGTCAAGGAAGATGTTGACAAAATTCCAATTTCA
TTTCTGCTTGGTTTTTTCGTTACAAATGTTATGACAAGATGGTGGTCGCAATTTCAATCA
ATTCCATCACCTGCAAAAGTTGCAGTTTATGTATCAGCATCAATTCATGGAAATGATGAA
GCTGGTCGAGTTATGAGAAGAACAATTATGAGATATGTCAATCTTTCACTTGTCATGGTT
TTTCGATTACTTTCACCAAGAGTCAAAACAAGATATCCCAAAATGGAAGATTTAATTGAA
GCCGGATTTATTACTGAAAGTGAACTTGCTGTTATGAAAAATATTGATCAAAAATATCCT
TCAACAAGTAAAAGTTGGCTACCGCTTTGTTGGGCTGCAAGTATTTGTAATAGAGCAAGA
GCAGAAGGTCGAATTAAAGATGATTTTGCATTGAAAACTTTGACTGATGAATTAAATAAT
TTTCGAGGCAATTTGGGTGCTTTGATGGATTTCAATGAATTTTGCATTCCATTGGTCTAT
GTGCAAGTTGTAACAATTGCTGTTTATACATTTTTCTTCACAACTGTCATTGCTAAGCAA
CCAATAATTCCTGAATACAATGAGAAATACAAAGAAACCCAATTTCTTGATCATCTTCCA
TTTTTGATTACGCTTCAATTTATTTTTTATATCGGTTGGTTGAAAGTCGCAGAGACAATG
ATAAATCCATTTGGTGAAGATGATGATGATTTTGATGTGAATTCAATGATTGATTCAAAT
TTAATTACAAGTTATTTAATTGTTGATGACATGCATAGTCAATATCCTGATTTACTTCGT
GATCGTTATTGGGATGCATTGCCGCGTGAACTTCCTGATATTGGAAAATTGGACAAAAAT
GAGAAAATAAAATTGACTGATTTCTTTGATGTTGTTGGAACTCGTAAAAGAAAATCAAGA
AAATCAAATTTGTTAATTCCACTCAATGAACAGGACAAAAAACAATTGTCAAGTGCATTT
TCATCTTTCAATTTTTCATCACAATCAAATAACATCACGACTGTGCCTAATTTTGGAAAT
ATTCAAACACAAGCAGAAAAGCAATTGCTAAAAACAAAACAAAGAGCAACAACAATTAAA
ATTAGTGAATTGAGCTCAAGTGATGATGATTGA
>g114.t1 Gene=g114 Length=450
MTVSYAEDLLSASGMSLIKLVFLKWKGSLFKLIWKDLLMFISMFYILQGIYVFGISEENK
KYFEGLVYYVKEDVDKIPISFLLGFFVTNVMTRWWSQFQSIPSPAKVAVYVSASIHGNDE
AGRVMRRTIMRYVNLSLVMVFRLLSPRVKTRYPKMEDLIEAGFITESELAVMKNIDQKYP
STSKSWLPLCWAASICNRARAEGRIKDDFALKTLTDELNNFRGNLGALMDFNEFCIPLVY
VQVVTIAVYTFFFTTVIAKQPIIPEYNEKYKETQFLDHLPFLITLQFIFYIGWLKVAETM
INPFGEDDDDFDVNSMIDSNLITSYLIVDDMHSQYPDLLRDRYWDALPRELPDIGKLDKN
EKIKLTDFFDVVGTRKRKSRKSNLLIPLNEQDKKQLSSAFSSFNFSSQSNNITTVPNFGN
IQTQAEKQLLKTKQRATTIKISELSSSDDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g114.t1 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 1 | 424 | 1.1E-151 |
| 3 | g114.t1 | PANTHER | PTHR10736 | BESTROPHIN | 1 | 424 | 1.1E-151 |
| 1 | g114.t1 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 20 | 321 | 1.7E-77 |
| 14 | g114.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 36 | - |
| 19 | g114.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 37 | 56 | - |
| 9 | g114.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 57 | 76 | - |
| 17 | g114.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 77 | 96 | - |
| 13 | g114.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 97 | 128 | - |
| 16 | g114.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 129 | 145 | - |
| 10 | g114.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 146 | 237 | - |
| 15 | g114.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 238 | 258 | - |
| 12 | g114.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 259 | 277 | - |
| 18 | g114.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 296 | - |
| 11 | g114.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 297 | 450 | - |
| 8 | g114.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 37 | 56 | - |
| 7 | g114.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 77 | 96 | - |
| 4 | g114.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 128 | 145 | - |
| 6 | g114.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 258 | - |
| 5 | g114.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 297 | - |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
