General information for g2872.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Bestrophin-1.
Parent gene
- The parent gene g2872 is located on chr_3: 20822582..20829511 (- 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 | g2872 | g2872.t4 | isoform | g2872.t4 | 20820599 | 20821616 |
| chr_3 | g2872 | g2872.t4 | exon | g2872.t4.exon1 | 20820599 | 20820728 |
| chr_3 | g2872 | g2872.t4 | cds | g2872.t4.CDS1 | 20820699 | 20820728 |
| chr_3 | g2872 | g2872.t4 | exon | g2872.t4.exon2 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t4 | cds | g2872.t4.CDS2 | 20820803 | 20820868 |
| chr_3 | g2872 | g2872.t4 | exon | g2872.t4.exon3 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t4 | cds | g2872.t4.CDS3 | 20820931 | 20821080 |
| chr_3 | g2872 | g2872.t4 | exon | g2872.t4.exon4 | 20821144 | 20821616 |
| chr_3 | g2872 | g2872.t4 | cds | g2872.t4.CDS4 | 20821144 | 20821167 |
| chr_3 | g2872 | g2872.t4 | TSS | g2872.t4 | NA | NA |
| chr_3 | g2872 | g2872.t4 | TTS | g2872.t4 | NA | NA |
Sequences
>g2872.t4 Gene=g2872 Length=819
TTGGAAACTTATCACCTAAAGTGAAAAAACGTTTTCCAACTTTAAATCATTACGTCGAAG
CAGGTCTTTTGAACGAAAATGAACGAGATATTATTGAAGATTTAAATAATAAATTTCCTC
GTCATTCCAAGCATTGGTTGCCAATAGTATGGGCTGCAAGTATAATCACTAGAGCTCGCA
AGGAAGGACGAATTCGTGATGATTTTGCTGTCAAGACAATTATCGATGAATTAAATAAAT
TTCGTGGACAATGTGGAGTGTTAATCGCCTATGACACTATTTCCATACCATTGGTTTACA
CTCAAGTTGTGACTATAGCTGTTTACTCTTACTTTTTGGTAGCTCTATTAGGACAGCAAT
GGACAGAAGGGAAAGGAACGGAAAATGGATATCAAAATCGATTTGATTTATACTTTCCAG
TATTCAGTCTTTTACAATTTTTTTTCTATATGGGATGGCTTAAAGTGGCAGAGCAACTTA
TAAATCCTTTCGGCGAAGATGACGATGATTTTGAAGTAAATTGGATGATTGATAGAAACC
TGCAGGTCAGCTATTTAATTGTAGATGATATTCATAATAGTCATCCAGAACTCATTAAAG
ATCAATATTGGGATAGTATTCTTGTACAAGATTTGCCATATACAGTTGCTTCAATGGGAA
ATCGAGAAAATCCACCAGAACCTTCAACAAGGTCAAAAAGGGTGGAGCTGAAATTGTGAC
CGCACCATCAGTGGCTAAAAACATGGATGATATGGTCGGTAAAAATACTGCAACTACAAA
TTATGAGTTTCCCGATAATGATAATGACAGTGATAAGGT
>g2872.t4 Gene=g2872 Length=89
MGWLKVAEQLINPFGEDDDDFEVNWMIDRNLQVSYLIVDDIHNSHPELIKDQYWDSILVQ
DLPYTVASMGNRENPPEPSTRSKRVELKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g2872.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 89 | - |
| 2 | g2872.t4 | PANTHER | PTHR10736:SF55 | BESTROPHIN 1, ISOFORM C-RELATED | 1 | 83 | 2.2E-39 |
| 3 | g2872.t4 | PANTHER | PTHR10736 | BESTROPHIN | 1 | 83 | 2.2E-39 |
| 1 | g2872.t4 | Pfam | PF01062 | Bestrophin, RFP-TM, chloride channel | 1 | 32 | 4.2E-15 |
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