General information for g12170.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Splicing factor 3B subunit 1.
Parent gene
- The parent gene g12170 is located on chr_1: 21450055..21451031 (- 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 | g12170 | g12170.t5 | isoform | g12170.t5 | 21448686 | 21450055 |
| chr_1 | g12170 | g12170.t5 | exon | g12170.t5.exon1 | 21448686 | 21449494 |
| chr_1 | g12170 | g12170.t5 | cds | g12170.t5.CDS1 | 21449351 | 21449494 |
| chr_1 | g12170 | g12170.t5 | exon | g12170.t5.exon2 | 21449558 | 21450055 |
| chr_1 | g12170 | g12170.t5 | cds | g12170.t5.CDS2 | 21449558 | 21449845 |
| chr_1 | g12170 | g12170.t5 | TSS | g12170.t5 | 21450082 | 21450082 |
| chr_1 | g12170 | g12170.t5 | TTS | g12170.t5 | NA | NA |
Sequences
>g12170.t5 Gene=g12170 Length=1307
ATGGAAGGTGAGCATAAAATTTTTGTTTTGAGTGAGAAATATGTGAAATAGAGATTTAAA
AATATCATAAACATTTAGATAAACATCTATTGCATAAATAAAATACAAATATAAAGTAGT
AAAATTGTTATTTCAAGTGAAAATACAAATTGTTGTAAACGTTTTGTCACTCATTGATTT
TTCACAAAACCGAAAAAAACATCCAGTAAAATGAATTCTATTGTCTTTTCAGATATCGAG
TCACAAATTAAAGACATTCAAGAGAAGAAACGACAGGCTCAAGCTCAAGAGGAGAGGCAG
AAAGGAATTGGATTATTAGAAAGTGGATATTTTGATTCAGAAATCTATGAGGGAGGACAA
AAAGGAAAATATGAGGGCTATGTAACATCAATTGCGACAAATGAAGAAGATGAGGACGAT
GATGATGAACCAATCAGACCAGATAAAAAGTCTTCAGCATTTAATGCTCCAATTTCATTT
ATTAAAGAAATCACAAGAAATGAACCAGAATATGATCCATTCGAGGATCGAAGACAAAAG
ACTGTTGGTGAAAAAGAAGATGAATATCGTCAGAGACGTAGAAAATTAGTCATTTCTCCA
GAACGTGTTGATCCTTTTGCTGATGGTAAGTGTCACTTGTAATTTTCTTATTTTTAATGC
ACTCTAGTGTTTAAGGATCTACTGCATATATGATACATATTTCTGTATAGAAACGAAAAA
GTTTGAATGAATGGTTTTTCATAAGAGTAAGATGGCCATTAAAAGGCGCCTGAATGAGAA
AATTCTTAGTTAGTATATAAGCAAATCATATTGTGCGCAAACTTTTATTAATGCGACCCA
ATTATCACAGGTATACTGCAGGCTTATCACAGATGGGAATAATATAAATGGTGCCATATC
GAGGTTATTAGAACCAAATTTTACAAAAAATAGTAGTGAAATTGTGGTGATACAATGACA
AGCTTTTTTCTTCATTAAAAACCATTTGATATTCTTTTTCATGTACTTTTAATTTCATGT
CACTTGTAACTCCACATTTTCATACACTGACTCGAATGACTGATGATGAATGTTTGTTAT
TTTATAAAAACCCTATTAATCGAAGAGAATTTATTCTAGGCAGTTTTGTTGGATGTGGAA
TTGATGGTGCAATTGTCTAGATGAAATATTTGAAAAATGATATTAATCCTAATCGTTTCT
AAAAATATTTTAAATGTTTTTCAAATATTTCTTTAGAAATTGCTAATAATCCCCTCTATC
ACGTACGTATGGTGAAAGATTTTTGAAATTTGTTAAAATTTTACACA
>g12170.t5 Gene=g12170 Length=143
MNSIVFSDIESQIKDIQEKKRQAQAQEERQKGIGLLESGYFDSEIYEGGQKGKYEGYVTS
IATNEEDEDDDDEPIRPDKKSSAFNAPISFIKEITRNEPEYDPFEDRRQKTVGEKEDEYR
QRRRKLVISPERVDPFADGKCHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g12170.t5 | Coils | Coil | Coil | 6 | 33 | - |
| 2 | g12170.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 63 | 123 | - |
| 1 | g12170.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 95 | 123 | - |
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.
