General information for g11612.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11612 is located on chr_1: 17445958..17446992 (+ 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 | g11612 | g11612.t2 | TSS | g11612.t2 | 17445900 | 17445900 |
| chr_1 | g11612 | g11612.t2 | isoform | g11612.t2 | 17445958 | 17446992 |
| chr_1 | g11612 | g11612.t2 | exon | g11612.t2.exon1 | 17445958 | 17446474 |
| chr_1 | g11612 | g11612.t2 | cds | g11612.t2.CDS1 | 17445958 | 17446474 |
| chr_1 | g11612 | g11612.t2 | exon | g11612.t2.exon2 | 17446538 | 17446992 |
| chr_1 | g11612 | g11612.t2 | cds | g11612.t2.CDS2 | 17446538 | 17446992 |
| chr_1 | g11612 | g11612.t2 | TTS | g11612.t2 | 17447040 | 17447040 |
Sequences
>g11612.t2 Gene=g11612 Length=972
ATGGTAAAAACTAAGAATCATTACATAAAATATAAATTAGCTGAATTGGAGAGTTACACT
AGAAACCCCGAATCATGTGTGAAAAAGATCAACTGCACAGAGAGGCTCAGATTCGCACCA
AACATTGTTGGAAATTTAAAAGAATCAATTTTAAGAATATTGAGCAGAAAAATTGGCAAA
TATGACATCAAAATGCAAGGAGTTGTTCTCGATTTCCGTAATACAAAAATATTAAATATA
TTAAATGATATTCGCAATGATTCAGCCTATTCAATCATCAATTTAAATAGTAATTTTTAT
ATATTTGCACCAAAAAAAGATGCTATCGTCGATGGGATAATCAAGCACGTAAATTTTCAA
AACATAGAAACAATTATAACAGTCGTAATTTTCCGAGTTTTTAATGTCAAAGTAATATTT
AAGGGATGTATCAAGAAGAGTCAAGTTCGAGAAAATGATGTGATTAAAATACGCATAAAA
AAATTTCATTTTGATAATGAAATTCCATATATTGAAGATGACAGTGGTGTCAGTGAAAGT
AGTTTAACATTTGAGTTAAATCCTCTTTTGAATATCAAAAAAGAACAAGAAGACATGTTT
GATAATATGAGTACATGTCCTACTCAATCAAAAGCATTGAAACGTAAGAGAATGAAATCA
CCGGAAAATATTGAAGAAGCTTTCATATCGAAAAAAATCAAACAAGAACCAATTGATTTT
GAAGACACTACCGACACGCAAGAGTTCATTCTAAATATTAAGCAGGAAATTCAAAATTGT
GAAAATAAAAGCAACAAAGATGAAATAAATATTAAAAATAAATCAGTACAAGATGCAAAT
GACAAGCTTAAAGAAAGTTCAAGCAAAAAGAAAAAGGAGAAAAAGAAAAAATATCGAAAA
GTTGAAGACGAATTTGAGACATCACTACAATTACTTTTCAATTCTTCAAGTATAAAAACC
GAAAAGAACTAA
>g11612.t2 Gene=g11612 Length=323
MVKTKNHYIKYKLAELESYTRNPESCVKKINCTERLRFAPNIVGNLKESILRILSRKIGK
YDIKMQGVVLDFRNTKILNILNDIRNDSAYSIINLNSNFYIFAPKKDAIVDGIIKHVNFQ
NIETIITVVIFRVFNVKVIFKGCIKKSQVRENDVIKIRIKKFHFDNEIPYIEDDSGVSES
SLTFELNPLLNIKKEQEDMFDNMSTCPTQSKALKRKRMKSPENIEEAFISKKIKQEPIDF
EDTTDTQEFILNIKQEIQNCENKSNKDEINIKNKSVQDANDKLKESSSKKKKEKKKKYRK
VEDEFETSLQLLFNSSSIKTEKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11612.t2 | Coils | Coil | Coil | 266 | 304 | - |
| 5 | g11612.t2 | Gene3D | G3DSA:3.30.1490.120 | - | 14 | 107 | 6.3E-6 |
| 3 | g11612.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 288 | - |
| 4 | g11612.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 299 | - |
| 1 | g11612.t2 | PANTHER | PTHR12709:SF5 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 | 17 | 296 | 1.2E-19 |
| 2 | g11612.t2 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 17 | 296 | 1.2E-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 transcript has been annotated with K03004 (DNA-directed RNA polymerase I subunit RPA43)
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.
