General information for g5974.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5974 is located on chr_2: 13119631..13120548 (- 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 | g5974 | g5974.t3 | TTS | g5974.t3 | 13118287 | 13118287 |
| chr_2 | g5974 | g5974.t3 | isoform | g5974.t3 | 13118295 | 13119061 |
| chr_2 | g5974 | g5974.t3 | exon | g5974.t3.exon1 | 13118295 | 13118439 |
| chr_2 | g5974 | g5974.t3 | cds | g5974.t3.CDS1 | 13118351 | 13118439 |
| chr_2 | g5974 | g5974.t3 | exon | g5974.t3.exon2 | 13118542 | 13119061 |
| chr_2 | g5974 | g5974.t3 | cds | g5974.t3.CDS2 | 13118542 | 13119010 |
| chr_2 | g5974 | g5974.t3 | TSS | g5974.t3 | 13119601 | 13119601 |
Sequences
>g5974.t3 Gene=g5974 Length=665
TATCAACAGAAAAAGGAACTGAAGGATCAAATTAAACAACTTAAAATTGCAATGGAAAGG
GATGATTCTGACGAAGACACAAAAAGAAATTTTTACTTGAAACTTATCAAATCATGCGTA
TGGGAGACACAAGATGAATTATCGACATTGGAACAAGAGTGTGAAATTCTCGAACATATC
GCGAAATTAAAGGAACATGACTCAGAATTTAGACGAGAACATGAATCAACTTCTAAAAAG
CCTCATCATTCACAAGTCGTTCCATTAAAGCCAATTATTATTACAAAAGATCAATTGCAA
AAAGCGGTTTACGGTGCTGGTTATCCATCTTTACCGACATATACTATTGAAGAATTTTAT
GATCAGCGTGTAGCAGCAGGCATTTTCCCAAATGCTGAGCAAGTTGCTAAACAAAATTCA
TTACAAGGACGTTGCGATATTGATCAAGAGGCGGAGCAAGCAAAAGAAGAAGAAGAAAAG
GAACAAAAAATGGAGCAAGATGATCCCGAATTATTACAACTCCCTCTCATATTTTCTTCC
TTTATTTACCACATTTATCTCTCAATATTGTCTCTCAAAAAAATAAATAAAAATTTTTAC
CTAAAATAATGCCTGCCTATGAAAAACGATTGGAACCAATAGGAGATGAAATAAAATTGT
AAAAA
>g5974.t3 Gene=g5974 Length=185
MERDDSDEDTKRNFYLKLIKSCVWETQDELSTLEQECEILEHIAKLKEHDSEFRREHEST
SKKPHHSQVVPLKPIIITKDQLQKAVYGAGYPSLPTYTIEEFYDQRVAAGIFPNAEQVAK
QNSLQGRCDIDQEAEQAKEEEEKEQKMEQDDPELLQLPLIFSSFIYHIYLSILSLKKINK
NFYLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5974.t3 | Coils | Coil | Coil | 130 | 151 | - |
| 3 | g5974.t3 | Gene3D | G3DSA:1.25.40.540 | - | 1 | 55 | 1.3E-8 |
| 2 | g5974.t3 | PANTHER | PTHR10933 | IMMUNOGLOBULIN-BINDING PROTEIN 1 | 5 | 151 | 2.4E-26 |
| 1 | g5974.t3 | Pfam | PF04177 | TAP42-like family | 2 | 150 | 4.2E-29 |
| 6 | g5974.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 153 | - |
| 7 | g5974.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 175 | - |
| 5 | g5974.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 176 | 185 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5974/g5974.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5974.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0009966 | regulation of signal transduction | BP |
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. There were no conditions that were differentially expressed