General information for g12340.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12340 is located on chr_1: 22643797..22644146 (+ 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_1 | g12340 | g12340.t4 | TSS | g12340.t4 | 22642413 | 22642413 |
| chr_1 | g12340 | g12340.t4 | isoform | g12340.t4 | 22642537 | 22643373 |
| chr_1 | g12340 | g12340.t4 | exon | g12340.t4.exon1 | 22642537 | 22642548 |
| chr_1 | g12340 | g12340.t4 | cds | g12340.t4.CDS1 | 22642537 | 22642548 |
| chr_1 | g12340 | g12340.t4 | exon | g12340.t4.exon2 | 22642632 | 22642883 |
| chr_1 | g12340 | g12340.t4 | cds | g12340.t4.CDS2 | 22642632 | 22642883 |
| chr_1 | g12340 | g12340.t4 | exon | g12340.t4.exon3 | 22642941 | 22643020 |
| chr_1 | g12340 | g12340.t4 | cds | g12340.t4.CDS3 | 22642941 | 22643020 |
| chr_1 | g12340 | g12340.t4 | exon | g12340.t4.exon4 | 22643087 | 22643308 |
| chr_1 | g12340 | g12340.t4 | cds | g12340.t4.CDS4 | 22643087 | 22643102 |
| chr_1 | g12340 | g12340.t4 | exon | g12340.t4.exon5 | 22643369 | 22643373 |
| chr_1 | g12340 | g12340.t4 | TTS | g12340.t4 | 22644285 | 22644285 |
Sequences
>g12340.t4 Gene=g12340 Length=571
ATGTACCCAAATTATCCAAATTCGAATCAACCTTATCCAAATATGCCACAATATCCAAAT
CAAATGCCTCCCTATCCGGATAATAATCAACAATATTTTCCACAAATGCCTGGAATGCCT
CAATATCAAATGCAGCCACAATATAATCCCATGCAACAGCAGTATCCTCCTCAAATGTCA
ACAGGACAATTTGATCAAAGTTATCAACAAGTTCATCATTATCAACAACAGCAGCAACCA
GCGATGAGTGTTCAACTAGCTCGGTCACGACCAACAGTCACACCAGCAGCTAATTTTGAC
GCAGCAAATGATGCCTCTATTTTACGGAAGGCTATGAAAGGTTTGTTTTGGAACAGATGA
AGCAGCAATCATAAATGTGTTATGTCGTCGACCATCACATCAAAGAATTGAAATTGCAAA
AGCATTTAAAACTGCATATGGCAAAGATTTAATTGAAAATATTCGTAAAGAAACATCAGG
AAACTTTGAAAGAGTGTTGGTTGCACTCTTGACACCAAAAATACAATATTATTGTGAAGA
ACTGTATGAAGCAATGGAAGGACAAGGCACT
>g12340.t4 Gene=g12340 Length=119
MYPNYPNSNQPYPNMPQYPNQMPPYPDNNQQYFPQMPGMPQYQMQPQYNPMQQQYPPQMS
TGQFDQSYQQVHHYQQQQQPAMSVQLARSRPTVTPAANFDAANDASILRKAMKGLFWNR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12340.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 81 | - |
| 3 | g12340.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 23 | - |
| 4 | g12340.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 81 | - |
| 1 | g12340.t4 | SUPERFAMILY | SSF47874 | Annexin | 61 | 115 | 1.01E-6 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005544 | calcium-dependent phospholipid binding | MF |
| GO:0005509 | calcium ion binding | MF |
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