General information for g5927.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5927 is located on chr_2: 12881941..12882919 (+ 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 | g5927 | g5927.t11 | isoform | g5927.t11 | 12881856 | 12882771 |
| chr_2 | g5927 | g5927.t11 | exon | g5927.t11.exon1 | 12881856 | 12882771 |
| chr_2 | g5927 | g5927.t11 | cds | g5927.t11.CDS1 | 12881875 | 12882414 |
| chr_2 | g5927 | g5927.t11 | TTS | g5927.t11 | 12882946 | 12882946 |
| chr_2 | g5927 | g5927.t11 | TSS | g5927.t11 | NA | NA |
Sequences
>g5927.t11 Gene=g5927 Length=916
TCTATGAAAATTATTGGAAATGAGCGGTAAGTTAAAATTGTTTATTTGTTTTAATTTTAC
GCTATTCAAGAACATTTTAATTGCAGAAAATACATCGGACGACCCTAGTTTATTAGTTAT
TGCTGTAGATACTAACCCATCTCAAATAGTAATCAGAAAAAATCCAGATGCTTTGACAAA
AATTATAAATTCAATTTCGGCATTTGGAAATGCTCATTTAATGCAAAAACCTCAAAACAA
ATTGGCTGTAGTTGCATGTCATCATCATGAAAGTAAATTTCTTTATCCGTCCGCTGAAAA
ACCTCAAGAATTTCGACAAATTGATGGTCAATATGAGTTTTTTACATTTGTGGAAAAGTC
AATTAAAAATAACTTGTCTGAATTGATAAAAAATGCTCCTAATATTTCAAATAATAGCGA
AAGTTTATTGGCTGGATGTCTTGCTATGATATTGTGCTATATATTAAGAGTAAGTAATAT
AAGATTCAACAGGAAAAAAGGTTCCAATTTAATTATTATTAATATTATAGATCAAGAAAT
CCCAACCAACAGGAAGTAATTTAAACACACGAATACTTGTTGTAACTGGCAGTGAAGACT
CAGCCCATCAATACATGACTTATATGAATGTATTCTTTACAGCACAAAAAGAAAGAGTTG
CTATTGACATTTGTGCTCTGGACAATACTTTAGTTTTACTTCAACAAGGTTGCGATATCA
CAGGAGGACATGTAATAATTTTTAATTTAAGAATAGTGATCTATTAACATTTGAATTTTG
TCTTTTAGTATTTAAAAGTTCCTCAGCTTGATGGACTTTTGCAATATTTACTCTGGATTT
TTCTTCCTGATCCATCAATTCGGTCTAAGCTTGCACTTCCGCCGCCCGTTAAAGTTGATT
ATCGTGCAGCATGCTT
>g5927.t11 Gene=g5927 Length=179
MSGKLKLFICFNFTLFKNILIAENTSDDPSLLVIAVDTNPSQIVIRKNPDALTKIINSIS
AFGNAHLMQKPQNKLAVVACHHHESKFLYPSAEKPQEFRQIDGQYEFFTFVEKSIKNNLS
ELIKNAPNISNNSESLLAGCLAMILCYILRVSNIRFNRKKGSNLIIINIIDQEIPTNRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5927.t11 | Gene3D | G3DSA:3.40.50.410 | - | 24 | 169 | 4.0E-31 |
| 2 | g5927.t11 | PANTHER | PTHR12831 | TRANSCRIPTION INITIATION FACTOR IIH TFIIH , POLYPEPTIDE 3-RELATED | 23 | 166 | 1.1E-18 |
| 1 | g5927.t11 | Pfam | PF03850 | Transcription factor Tfb4 | 29 | 166 | 1.6E-27 |
| 6 | g5927.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 134 | - |
| 7 | g5927.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 135 | 152 | - |
| 5 | g5927.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 153 | 179 | - |
| 3 | g5927.t11 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5927/g5927.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5927.t11.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0000439 | transcription factor TFIIH core complex | CC |
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.
