Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g2872.t6 20821616 20829373
chr_3 g2872 g2872.t6 exon g2872.t6.exon1 20821616 20821620
chr_3 g2872 g2872.t6 cds g2872.t6.CDS1 20821618 20821620
chr_3 g2872 g2872.t6 exon g2872.t6.exon2 20821678 20821731
chr_3 g2872 g2872.t6 cds g2872.t6.CDS2 20821678 20821731
chr_3 g2872 g2872.t6 exon g2872.t6.exon3 20822490 20822781
chr_3 g2872 g2872.t6 cds g2872.t6.CDS3 20822490 20822781
chr_3 g2872 g2872.t6 exon g2872.t6.exon4 20828267 20828306
chr_3 g2872 g2872.t6 cds g2872.t6.CDS4 20828267 20828306
chr_3 g2872 g2872.t6 exon g2872.t6.exon5 20828371 20828621
chr_3 g2872 g2872.t6 cds g2872.t6.CDS5 20828371 20828401
chr_3 g2872 g2872.t6 exon g2872.t6.exon6 20829344 20829373
chr_3 g2872 g2872.t6 TSS g2872.t6 20829511 20829511
chr_3 g2872 g2872.t6 TTS g2872.t6 NA NA

Sequences

>g2872.t6 Gene=g2872 Length=672
TTTTTAAAGTATTAGTGTCCACAATATCGTATCGAAGCTATGATCGTCACGCAAAATTAT
TAGAACTCTTATAAAATATAGTTAATAGTGATAACTAAAGAACTGAAAAATGAGATGATA
TTAAAGCACAAGTGAAAACTATTTAATGTGTGTGTTGTGCAAATTATTTTTGTCAATATA
TTGAAAAAGAATCTTTTGTGAGGTCACTTCAACATCAATTTGTGTTATTTATAAGAAGAA
AAGTATTATAATGACTGTATCATATACTGGACAAGTAGCAACGTGTAAGGGCTTCGGCTG
TTTCTTAAAACTGCTTTGGAGATGGCGAGGATCAATTTATAAATTACTTTGGCTTGACTT
AACATCATTTCTCTTAATATACTACACATTAAATCTAACTTACCGCCTTGCACTTAATGA
AGATCAGAAAAAAACATTTGAAGCTTTAGTAAAATATTGCGATGAACATTCCAATCTTAT
TCCACTATCATTTGTCCTCGGTTTTTATGTGTCGATAGTCATGACTAGATGGTGGAATCA
ATACACTTCAATTCCGTGGCCAGATCCAATTGCAGTCTTTGTAAGTGCAACCGTTCATGG
TCAGGACGAGCGAGGTAGAGTGATGCGCAGAACAATTATGCGATATGTATGTTTGTGCAT
AAGTATGGTACT

>g2872.t6 Gene=g2872 Length=140
MTVSYTGQVATCKGFGCFLKLLWRWRGSIYKLLWLDLTSFLLIYYTLNLTYRLALNEDQK
KTFEALVKYCDEHSNLIPLSFVLGFYVSIVMTRWWNQYTSIPWPDPIAVFVSATVHGQDE
RGRVMRRTIMRYVCLCISMV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g2872.t6 PANTHER PTHR10736:SF55 BESTROPHIN 1, ISOFORM C-RELATED 1 140 2.1E-76
3 g2872.t6 PANTHER PTHR10736 BESTROPHIN 1 140 2.1E-76
1 g2872.t6 Pfam PF01062 Bestrophin, RFP-TM, chloride channel 9 139 4.1E-36
7 g2872.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 31 -
9 g2872.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 55 -
6 g2872.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 56 75 -
10 g2872.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -
8 g2872.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 96 140 -
5 g2872.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
4 g2872.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -

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.

Raw TPM values