General information for g2871.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bestrophin-2.
Parent gene
- The parent gene g2871 is located on chr_3: 20816897..20818642 (- 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 | g2871 | g2871.t1 | isoform | g2871.t1 | 20816897 | 20818642 |
| chr_3 | g2871 | g2871.t1 | exon | g2871.t1.exon1 | 20816897 | 20817379 |
| chr_3 | g2871 | g2871.t1 | cds | g2871.t1.CDS1 | 20816897 | 20817379 |
| chr_3 | g2871 | g2871.t1 | exon | g2871.t1.exon2 | 20817444 | 20817613 |
| chr_3 | g2871 | g2871.t1 | cds | g2871.t1.CDS2 | 20817444 | 20817613 |
| chr_3 | g2871 | g2871.t1 | exon | g2871.t1.exon3 | 20817811 | 20817972 |
| chr_3 | g2871 | g2871.t1 | cds | g2871.t1.CDS3 | 20817811 | 20817972 |
| chr_3 | g2871 | g2871.t1 | exon | g2871.t1.exon4 | 20818033 | 20818299 |
| chr_3 | g2871 | g2871.t1 | cds | g2871.t1.CDS4 | 20818033 | 20818299 |
| chr_3 | g2871 | g2871.t1 | exon | g2871.t1.exon5 | 20818369 | 20818642 |
| chr_3 | g2871 | g2871.t1 | cds | g2871.t1.CDS5 | 20818369 | 20818642 |
| chr_3 | g2871 | g2871.t1 | TSS | g2871.t1 | NA | NA |
| chr_3 | g2871 | g2871.t1 | TTS | g2871.t1 | NA | NA |
Sequences
>g2871.t1 Gene=g2871 Length=1356
ATGACAGTTACATATACTGATCAAATTGCAACTGCAAAAGGTCTAACGCTTTTAAAATTA
ATGTTCTTTAAATGGCGTGGATCACTTCTTCGTTTAGTGTGGAAAGATTTAATTGTTTTT
GTTTCGATACATTATGTGATTCAAATAATTTATAAATATATACTCAACGATGATAGTAGA
AATTATTTGGATTGCTTTTTTAGTCATGTTCAAGAATATCAAAAAATGATACCGCTTTCT
TTTGTGCTTGGTTTTTTCGTTTCAACTGTCTCAGTACGATGGTGGAATCAATTTGAATCA
ATTCCTTGGCCCACTCATATAGCAGTTTATGTGTCAAGCACTCTACATGGATATGATGAA
GTTGGACGTGCTATGCGTAGAACAATTTTGCGATATGTTAATTTATCATTGGTCATGGTT
TTTCGTGCACTCTCACCTAGAGTGAAGAAGAGATTTCCAAAAATGGACGACCTAATTACT
GCTGGATTTATTAATGAAAGTGAATTATCAGTTTTGCAAGATATTGAAAAGAAGTATCCT
GGCTATAATAAGAACTGGCTGCCAATTTGTTGGGCTGCAAATTTAGCAACACGTGCTCGA
GACGATGGTCGAATTAAAGACGATTTTGCTTTGAAAACAATAATAGAAGAACTTAACAAA
TTTCGAGCTCATTGTGGTGCTTTGATGAATTATGCTTATATTTGTTTACCATTGGTTTAT
ATTCAAGTTGTGACTTTAGCTACATATACTTATTTTATATTGCTACTCATTCAAATACCG
AGAAAAAATGAAAACGAAGGATCTTTTAATTTTCTACCAATTCTTATTTCACTTCAGTTT
GTATTTTATATGGGATGGCTTAAAGTGGCAGAAACAATGATAAATCCTTTTGGAGATGAT
GACGATGATTTTGAAGTGAATAATATGATTGATAAAAATTTGATTATAAGTTATTTAATT
GTCGACATCATGCATGATGATCATCCTGAGCTGTTGAAAGATCAATATTGGGATGGAATT
CCAAGTACATTACCTGATCGTGGTCGAGTTCATCCTAAAGATTTTGAAATTAGTCATATC
ACTGACTTTTTTGATGTGAAAGATGAAAACGATACAAAGACAACACCGGTTGCTTATCAA
GATGCTAATCAAGAAGCAAATAGATTTTCAATGTATCAAGTTAAGTTTGATCAAATACCT
CGATCATCAGTGATTGATGAAACTTATAGAAGAGTTTCAAATGTTGAAATATCACAAAGT
CACTTACAACGTCAAATGCAAAAAGCTCGAGAAAAAGTTCTATCAAGACAAATCTCTTAT
GAAACATCAACTGAAACTTTAAATCCTCATTTATAA
>g2871.t1 Gene=g2871 Length=451
MTVTYTDQIATAKGLTLLKLMFFKWRGSLLRLVWKDLIVFVSIHYVIQIIYKYILNDDSR
NYLDCFFSHVQEYQKMIPLSFVLGFFVSTVSVRWWNQFESIPWPTHIAVYVSSTLHGYDE
VGRAMRRTILRYVNLSLVMVFRALSPRVKKRFPKMDDLITAGFINESELSVLQDIEKKYP
GYNKNWLPICWAANLATRARDDGRIKDDFALKTIIEELNKFRAHCGALMNYAYICLPLVY
IQVVTLATYTYFILLLIQIPRKNENEGSFNFLPILISLQFVFYMGWLKVAETMINPFGDD
DDDFEVNNMIDKNLIISYLIVDIMHDDHPELLKDQYWDGIPSTLPDRGRVHPKDFEISHI
TDFFDVKDENDTKTTPVAYQDANQEANRFSMYQVKFDQIPRSSVIDETYRRVSNVEISQS
HLQRQMQKAREKVLSRQISYETSTETLNPHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2871.t1 | Coils | Coil | Coil | 412 | 432 | - |
| 2 | g2871.t1 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 1 | 430 | 9.7E-155 |
| 3 | g2871.t1 | PANTHER | PTHR10736 | BESTROPHIN | 1 | 430 | 9.7E-155 |
| 1 | g2871.t1 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 10 | 314 | 1.7E-81 |
| 13 | g2871.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 36 | - |
| 19 | g2871.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 37 | 55 | - |
| 9 | g2871.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 56 | 75 | - |
| 18 | g2871.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 95 | - |
| 14 | g2871.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 96 | 128 | - |
| 16 | g2871.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 129 | 145 | - |
| 11 | g2871.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 146 | 230 | - |
| 15 | g2871.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 257 | - |
| 12 | g2871.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 258 | 268 | - |
| 17 | g2871.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 269 | 287 | - |
| 10 | g2871.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 288 | 451 | - |
| 4 | g2871.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 51 | - |
| 7 | g2871.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 95 | - |
| 5 | g2871.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 253 | - |
| 6 | g2871.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 287 | - |
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