General information for g3121.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bestrophin-2.
Parent gene
- The parent gene g3121 is located on chr_3: 22937178..22938659 (- 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 | g3121 | g3121.t1 | TTS | g3121.t1 | 22937169 | 22937169 |
| chr_3 | g3121 | g3121.t1 | isoform | g3121.t1 | 22937178 | 22938659 |
| chr_3 | g3121 | g3121.t1 | exon | g3121.t1.exon1 | 22937178 | 22937608 |
| chr_3 | g3121 | g3121.t1 | cds | g3121.t1.CDS1 | 22937178 | 22937608 |
| chr_3 | g3121 | g3121.t1 | exon | g3121.t1.exon2 | 22937662 | 22937685 |
| chr_3 | g3121 | g3121.t1 | cds | g3121.t1.CDS2 | 22937662 | 22937685 |
| chr_3 | g3121 | g3121.t1 | exon | g3121.t1.exon3 | 22937756 | 22938659 |
| chr_3 | g3121 | g3121.t1 | cds | g3121.t1.CDS3 | 22937756 | 22938659 |
| chr_3 | g3121 | g3121.t1 | TSS | g3121.t1 | NA | NA |
Sequences
>g3121.t1 Gene=g3121 Length=1359
ATGACTGTTAGTTATTCAGATTCAGTCACAACAACAAATCCATGGACATTTTTGAAACTT
CTCATAAGATGGAAAGGCTCAGTTTATAAACTTTTATGGAGAGAATTGCTGTTTTATTTA
GCATTATTTTATGCCATTCACTTCATTTATATCTATTTACCAAAAGATCATCAAGCAAAT
TTTGAATCTTTTGTCAAATACACTAAACTTTATCAAAATATAATTCCAATTTCATTTGTG
CTTGGTTTCTTTGTCAATACAGTAATGACACGGTGGTGGAATCATTTTGAAGCAATTCCT
TATCCACTATCAATTGCAATTCATATTTCATGTAAATTACAAGGATATGATGAAGTTGGA
CGTGCAATGAGAAGAACAATTATGCGATATGTTTGTTTGAGTCTCACTTTGGTTTTTCGA
AGACTTTCTACTCGAGTTCAATTACGTTTTCCAAAATTCAAAGATTTAGTTATTGCTGGA
TTAATGTTTGATAGTGAAGTTCAGATTATTGAAGATGTAGAAGCAAAATATCCTGGTTAT
AGTAAAAACTGGCTGCCAATAACTTGGGCTGCAAATATTGTTGCAAAAGCAAGAAATGAA
GGAAGAATTGACGATGATGTGACAGTTAATGAAATTATTCACGAACTCAATGCATTCCGA
CAAAAGTTAACAGTTCTTTTGTATTATAATACAATCACAATTCCACTGGTCTATACTCAA
GTCGTTACTGCATCTTTATACATATATTTCTTAGCAGCATTATTTTCACATCAACATATT
CAATCAGACACATCTTATAATATTGGATCATTTAATTTAGACATTCATCCAATATTGCTC
ATTCTTCAATTTATTTTTCATATTGGTTGGCTAAAAGTCGGGCAAGCTCTAGTGAATCCG
TTCGGTATGGATGACGATGATTTTGATGTGAACTCAATGATTGACAGAAATTTACAATCA
AGTTACATAATTGTTGATAATATGCACAATAGTTATCCAGATATACTAAAAGATCGTTAT
TGGAATGAGCTACCAAAATATTTGCCTGATCGTGCAAAGACAGTTTTTCAAATTAATTCC
CCAAAAGCAGTAAATGATGCTGATGTTGTTGACTACACAGAACCACGACCTACAACTTGG
AATGATCTTGAAAAAAGTAATGCTTCATATGCAGTCATTAGAGTGAATGCGCCAATAAAC
TTAGTTCCTGATTCTGGAGTGATTGCACATGTTTATAAAAATATTGATAATGTCGAGCAT
GAACAACTCTTGATAAACAGAGCAATGCAAAGAAAATCTCAAAATCGTGATTCAAATTTA
TCTGAAGAAAGTGAAGAATCAATCAGAGAAAGTAAATAA
>g3121.t1 Gene=g3121 Length=452
MTVSYSDSVTTTNPWTFLKLLIRWKGSVYKLLWRELLFYLALFYAIHFIYIYLPKDHQAN
FESFVKYTKLYQNIIPISFVLGFFVNTVMTRWWNHFEAIPYPLSIAIHISCKLQGYDEVG
RAMRRTIMRYVCLSLTLVFRRLSTRVQLRFPKFKDLVIAGLMFDSEVQIIEDVEAKYPGY
SKNWLPITWAANIVAKARNEGRIDDDVTVNEIIHELNAFRQKLTVLLYYNTITIPLVYTQ
VVTASLYIYFLAALFSHQHIQSDTSYNIGSFNLDIHPILLILQFIFHIGWLKVGQALVNP
FGMDDDDFDVNSMIDRNLQSSYIIVDNMHNSYPDILKDRYWNELPKYLPDRAKTVFQINS
PKAVNDADVVDYTEPRPTTWNDLEKSNASYAVIRVNAPINLVPDSGVIAHVYKNIDNVEH
EQLLINRAMQRKSQNRDSNLSEESEESIRESK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3121.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 429 | 452 | - |
| 8 | g3121.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 436 | 452 | - |
| 2 | g3121.t1 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 1 | 404 | 1.1E-146 |
| 3 | g3121.t1 | PANTHER | PTHR10736 | BESTROPHIN | 1 | 404 | 1.1E-146 |
| 1 | g3121.t1 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 9 | 319 | 7.2E-80 |
| 15 | g3121.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 35 | - |
| 17 | g3121.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 53 | - |
| 12 | g3121.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 54 | 73 | - |
| 20 | g3121.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 93 | - |
| 14 | g3121.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 94 | 126 | - |
| 19 | g3121.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 143 | - |
| 10 | g3121.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 144 | 225 | - |
| 18 | g3121.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 255 | - |
| 13 | g3121.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 256 | 274 | - |
| 16 | g3121.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 275 | 293 | - |
| 11 | g3121.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 294 | 452 | - |
| 5 | g3121.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 53 | - |
| 7 | g3121.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 93 | - |
| 6 | g3121.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 256 | - |
| 4 | g3121.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 269 | 291 | - |
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. There were no conditions that were differentially expressed