General information for g10189.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g10189 is located on chr_1: 8155612..8156618 (- 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 | g10189 | g10189.t1 | TTS | g10189.t1 | 8155349 | 8155349 |
| chr_1 | g10189 | g10189.t1 | isoform | g10189.t1 | 8155612 | 8156618 |
| chr_1 | g10189 | g10189.t1 | exon | g10189.t1.exon1 | 8155612 | 8155746 |
| chr_1 | g10189 | g10189.t1 | cds | g10189.t1.CDS1 | 8155612 | 8155746 |
| chr_1 | g10189 | g10189.t1 | exon | g10189.t1.exon2 | 8155803 | 8156451 |
| chr_1 | g10189 | g10189.t1 | cds | g10189.t1.CDS2 | 8155803 | 8156451 |
| chr_1 | g10189 | g10189.t1 | exon | g10189.t1.exon3 | 8156512 | 8156618 |
| chr_1 | g10189 | g10189.t1 | cds | g10189.t1.CDS3 | 8156512 | 8156618 |
| chr_1 | g10189 | g10189.t1 | TSS | g10189.t1 | NA | NA |
Sequences
>g10189.t1 Gene=g10189 Length=891
ATGCATAACTCATTAATTAACACAAATTCTAATTCAATGTATCGTCGAGCCGTTTCACAA
CAATCTGAGTACAAATCGAAACTTTTTGATGAGATTGCTATTTTAATGCGCGCGAATGGT
GACTGTGATGTTCATATGCAGTTGAAGGAATCAATAATTCTAGTGGAGAAAATACTGATA
CAGCAGCTAAAAGCTTTAATTTTTGAGGCCATTGAAGTCTCTAACAATCCATCACCACAA
CTAACAGATTTTGAGTTTTTACTTCATCGAAATAAGCCTAAATTAGCTAGATTCCGAAAT
CATATGAAAAATGTACAAAAAATTCAATGTAAAAGCGATCAAAAGCAACTTGGATTAGAC
CCAACCTTCCTTAATCGGATATCTTCTGAAGAGAGTGATGAAGAGCAAGAAATTTATGAT
GCGGAAAAGACAAGGCGTATTTATCGAGCTGATAGAATCTCACAGATATTAAGTCCACAA
AAATATGACGAGTTTCAAAAAGCACGCAGCTACACGAGCAATCTAAGAAATAAAAATAAT
TTTCTTAACAAACTTGTTGAAGTTCTGCAGATACCTAAGGAGTTGCAAGAAAATAGTCCT
AATTTTCTTGATTGCCTACTATTTTTTGCTCTTGAAACAGTTGCAACCTTGGTAGATTTC
TCTATTTTAACTCGATTAAATTCTGATAATCGCATTAATGATCCAATTATTGTTCCTTCA
AATTTATCTAATGATATTTTGCATATATGTCCTGAGGTCACACAGGGAAGAGGACAAGAG
GGAATAAAACCAATAAAAGTTCAAGAAATACAAGAAGCAATGCGAAGAGTTCAACAAATG
CATAATCATAGAAAAATGGGCTCTTCTAAAATTGCTTTTCTCGCTCTCTAA
>g10189.t1 Gene=g10189 Length=296
MHNSLINTNSNSMYRRAVSQQSEYKSKLFDEIAILMRANGDCDVHMQLKESIILVEKILI
QQLKALIFEAIEVSNNPSPQLTDFEFLLHRNKPKLARFRNHMKNVQKIQCKSDQKQLGLD
PTFLNRISSEESDEEQEIYDAEKTRRIYRADRISQILSPQKYDEFQKARSYTSNLRNKNN
FLNKLVEVLQIPKELQENSPNFLDCLLFFALETVATLVDFSILTRLNSDNRINDPIIVPS
NLSNDILHICPEVTQGRGQEGIKPIKVQEIQEAMRRVQQMHNHRKMGSSKIAFLAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g10189.t1 | PANTHER | PTHR11380:SF5 | TRANSCRIPTION INITIATION PROTEIN SPT3 HOMOLOG | 10 | 279 | 0e+00 |
| 3 | g10189.t1 | PANTHER | PTHR11380 | TRANSCRIPTION INITIATION FACTOR TFIID/SUPT3-RELATED | 10 | 279 | 0e+00 |
| 1 | g10189.t1 | Pfam | PF02269 | Transcription initiation factor IID, 18kD subunit | 30 | 108 | 6e-07 |
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:0006366 | transcription by RNA polymerase II | BP |
KEGG
Orthology
- This transcript has been annotated with K11313 (transcription initiation protein SPT3)
Pathway
- This transcript belongs to the following pathways
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.
