General information for g6546.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative General transcription and DNA repair factor IIH helicase subunit XPB.
Parent gene
- The parent gene g6546 is located on chr_2: 17575870..17578240 (- 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_2 | g6546 | g6546.t12 | TTS | g6546.t12 | 17575795 | 17575795 |
| chr_2 | g6546 | g6546.t12 | isoform | g6546.t12 | 17575805 | 17576453 |
| chr_2 | g6546 | g6546.t12 | exon | g6546.t12.exon1 | 17575805 | 17576453 |
| chr_2 | g6546 | g6546.t12 | cds | g6546.t12.CDS1 | 17575870 | 17576202 |
| chr_2 | g6546 | g6546.t12 | TSS | g6546.t12 | NA | NA |
Sequences
>g6546.t12 Gene=g6546 Length=649
CACTGCAAAATGAAAGAATTCAAATTCTTCAGAATTTCAAATTCAATCCAAAAGTGAACA
CAATTTTTGTGAGTAAAGTTGCCGACACTAGTTTCGATTTGCCAGAAGCAAATGTTTTGA
TTCAAATATCTTCACATGGTGGTTCGAGACGTCAAGAAGCTCAACGTTTAGGTCGTATTT
TACGTGCAAAGAAAGGATCTTTTGCAGAAGAATATAATGCATTTTTCTACACTCTTGTTT
CACAAGACACAATGGAAATGAGTTATTCAAGAAAACGTCAAAGATTTTTGGTTAATCAGG
GTTACAGTTACAAAGTGATTACTCATTTAAGTGGAATGGACGAAGATCAAAGTCTCTTCT
ATAAGACACGAGAAGAGCAAGGACAATTGCTGCAACAAGTTTTAGCAGCATCTGATATAG
ATTGTGAAGATGAAAAAGTTCCTGGTGAAATTGGCGGATCAAGACCAGGTACTTCTAGAA
AAACTGGTGGTTTTAGTTCACTTTCTGGTGCTGACAATGAGGTTTACTTTGAACAAAAGA
AGAAAAGTAGTGTTCAACATCCACTTTTTAAAAGATTCCGTTAAGTTTAAAGAACTTTTT
TTGCTACATTATGTATGTTGTGTATGAAACATTTATTAAAACAATTCTT
>g6546.t12 Gene=g6546 Length=110
MEMSYSRKRQRFLVNQGYSYKVITHLSGMDEDQSLFYKTREEQGQLLQQVLAASDIDCED
EKVPGEIGGSRPGTSRKTGGFSSLSGADNEVYFEQKKKSSVQHPLFKRFR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6546.t12 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 64 | 2.0E-9 |
| 3 | g6546.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 63 | 82 | - |
| 2 | g6546.t12 | PANTHER | PTHR11274 | RAD25/XP-B DNA REPAIR HELICASE | 2 | 107 | 1.6E-15 |
| 1 | g6546.t12 | Pfam | PF16203 | ERCC3/RAD25/XPB C-terminal helicase | 2 | 67 | 1.5E-19 |
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.
