Gene loci information

Transcript annotation

  • This transcript has been annotated as Bestrophin-2.

Parent gene

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.t2 isoform g2872.t2 20820393 20829511
chr_3 g2872 g2872.t2 exon g2872.t2.exon1 20820393 20820738
chr_3 g2872 g2872.t2 cds g2872.t2.CDS1 20820571 20820738
chr_3 g2872 g2872.t2 exon g2872.t2.exon2 20820803 20820868
chr_3 g2872 g2872.t2 cds g2872.t2.CDS2 20820803 20820868
chr_3 g2872 g2872.t2 exon g2872.t2.exon3 20820931 20821080
chr_3 g2872 g2872.t2 cds g2872.t2.CDS3 20820931 20821080
chr_3 g2872 g2872.t2 exon g2872.t2.exon4 20821144 20821620
chr_3 g2872 g2872.t2 cds g2872.t2.CDS4 20821144 20821620
chr_3 g2872 g2872.t2 exon g2872.t2.exon5 20821678 20821731
chr_3 g2872 g2872.t2 cds g2872.t2.CDS5 20821678 20821731
chr_3 g2872 g2872.t2 exon g2872.t2.exon6 20822490 20822781
chr_3 g2872 g2872.t2 cds g2872.t2.CDS6 20822490 20822781
chr_3 g2872 g2872.t2 exon g2872.t2.exon7 20828267 20828306
chr_3 g2872 g2872.t2 cds g2872.t2.CDS7 20828267 20828306
chr_3 g2872 g2872.t2 exon g2872.t2.exon8 20828371 20828621
chr_3 g2872 g2872.t2 cds g2872.t2.CDS8 20828371 20828401
chr_3 g2872 g2872.t2 exon g2872.t2.exon9 20829344 20829511
chr_3 g2872 g2872.t2 TSS g2872.t2 20829511 20829511
chr_3 g2872 g2872.t2 TTS g2872.t2 NA NA

Sequences

>g2872.t2 Gene=g2872 Length=1844
AGTTTGAGGTTTAACTTTATCAAGATAAGACGTGTTTTATAATTTCTCTTTACGTAAATT
AACATGAAATAAAACTCTAATTATTTATTTGCCAAGTGTATGTGTAGATGTCAGATCTTT
ATAATTGTTCTAGAGTCATTTTTAAAGTATTAGTGTCCACAATATCGTATCGAAGCTATG
ATCGTCACGCAAAATTATTAGAACTCTTATAAAATATAGTTAATAGTGATAACTAAAGAA
CTGAAAAATGAGATGATATTAAAGCACAAGTGAAAACTATTTAATGTGTGTGTTGTGCAA
ATTATTTTTGTCAATATATTGAAAAAGAATCTTTTGTGAGGTCACTTCAACATCAATTTG
TGTTATTTATAAGAAGAAAAGTATTATAATGACTGTATCATATACTGGACAAGTAGCAAC
GTGTAAGGGCTTCGGCTGTTTCTTAAAACTGCTTTGGAGATGGCGAGGATCAATTTATAA
ATTACTTTGGCTTGACTTAACATCATTTCTCTTAATATACTACACATTAAATCTAACTTA
CCGCCTTGCACTTAATGAAGATCAGAAAAAAACATTTGAAGCTTTAGTAAAATATTGCGA
TGAACATTCCAATCTTATTCCACTATCATTTGTCCTCGGTTTTTATGTGTCGATAGTCAT
GACTAGATGGTGGAATCAATACACTTCAATTCCGTGGCCAGATCCAATTGCAGTCTTTGT
AAGTGCAACCGTTCATGGTCAGGACGAGCGAGGTAGAGTGATGCGCAGAACAATTATGCG
ATATGTATGTTTGTGCATAAGTATGGTACTTGGAAACTTATCACCTAAAGTGAAAAAACG
TTTTCCAACTTTAAATCATTACGTCGAAGCAGGTCTTTTGAACGAAAATGAACGAGATAT
TATTGAAGATTTAAATAATAAATTTCCTCGTCATTCCAAGCATTGGTTGCCAATAGTATG
GGCTGCAAGTATAATCACTAGAGCTCGCAAGGAAGGACGAATTCGTGATGATTTTGCTGT
CAAGACAATTATCGATGAATTAAATAAATTTCGTGGACAATGTGGAGTGTTAATCGCCTA
TGACACTATTTCCATACCATTGGTTTACACTCAAGTTGTGACTATAGCTGTTTACTCTTA
CTTTTTGGTAGCTCTATTAGGACAGCAATGGACAGAAGGGAAAGGAACGGAAAATGGATA
TCAAAATCGATTTGATTTATACTTTCCAGTATTCAGTCTTTTACAATTTTTTTTCTATAT
GGGATGGCTTAAAGTGGCAGAGCAACTTATAAATCCTTTCGGCGAAGATGACGATGATTT
TGAAGTAAATTGGATGATTGATAGAAACCTGCAGGTCAGCTATTTAATTGTAGATGATAT
TCATAATAGTCATCCAGAACTCATTAAAGATCAATATTGGGATAGTATTCTTGTACAAGA
TTTGCCATATACAGTTGCTTCAATGGGAAATCGAGAAAATCCACCAGAACCTTCAACAGC
AAATGTAGAGGTCAAAAAGGGTGGAGCTGAAATTGTGACCGCACCATCAGTGGCTAAAAA
CATGGATGATATGGTCGGTAAAAATACTGCAACTACAAATTATGAGTTTCCCGATAATGA
TAATGACAGTGATAAGGTTAGCCGCGTTTCAAAATTCTTCAAATGATCTCAAAATTTTCT
AAAGTTTCTATCACATTCTCTATCTAATCATATGTACAATAAAAAATTTAAAATTTCTTT
TATTCTCATTTTATTCCAAATTGGTGAAGGAAAAAATGCTAAAAATACCATGCACAGTAC
ACACAACAAAATCAGGCTTGTTTGCGACACAGCTATCCAATGTC

>g2872.t2 Gene=g2872 Length=425
MTVSYTGQVATCKGFGCFLKLLWRWRGSIYKLLWLDLTSFLLIYYTLNLTYRLALNEDQK
KTFEALVKYCDEHSNLIPLSFVLGFYVSIVMTRWWNQYTSIPWPDPIAVFVSATVHGQDE
RGRVMRRTIMRYVCLCISMVLGNLSPKVKKRFPTLNHYVEAGLLNENERDIIEDLNNKFP
RHSKHWLPIVWAASIITRARKEGRIRDDFAVKTIIDELNKFRGQCGVLIAYDTISIPLVY
TQVVTIAVYSYFLVALLGQQWTEGKGTENGYQNRFDLYFPVFSLLQFFFYMGWLKVAEQL
INPFGEDDDDFEVNWMIDRNLQVSYLIVDDIHNSHPELIKDQYWDSILVQDLPYTVASMG
NRENPPEPSTANVEVKKGGAEIVTAPSVAKNMDDMVGKNTATTNYEFPDNDNDSDKVSRV
SKFFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g2872.t2 PANTHER PTHR10736:SF55 BESTROPHIN 1, ISOFORM C-RELATED 1 394 1.7E-215
3 g2872.t2 PANTHER PTHR10736 BESTROPHIN 1 394 1.7E-215
1 g2872.t2 Pfam PF01062 Bestrophin, RFP-TM, chloride channel 9 322 4.6E-96
11 g2872.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 31 -
15 g2872.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 55 -
9 g2872.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 56 75 -
16 g2872.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -
13 g2872.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 96 128 -
17 g2872.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 129 146 -
10 g2872.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 237 -
18 g2872.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 238 257 -
12 g2872.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 258 276 -
14 g2872.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 277 294 -
8 g2872.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 295 425 -
7 g2872.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
5 g2872.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -
6 g2872.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 234 256 -
4 g2872.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 277 294 -

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

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.

Raw TPM values