General information for g5974.t9
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.t9 | TTS | g5974.t9 | 13118287 | 13118287 |
| chr_2 | g5974 | g5974.t9 | isoform | g5974.t9 | 13118854 | 13119631 |
| chr_2 | g5974 | g5974.t9 | exon | g5974.t9.exon1 | 13118854 | 13119631 |
| chr_2 | g5974 | g5974.t9 | cds | g5974.t9.CDS1 | 13118855 | 13119391 |
| chr_2 | g5974 | g5974.t9 | TSS | g5974.t9 | 13119601 | 13119601 |
Sequences
>g5974.t9 Gene=g5974 Length=778
ATGGAAGAAATAAAGTTACAAGAATTATTTAGTGATGCATATAAATTATTTGAAACCTTT
GATACACGTGACGATCCCACCAATAGCCCAGAATTTCAAGTAAGTACGATTTCATCACTT
AATTGATCAAGTTTAAGAGTTTTCCAGAAATATCGAAATAGCATTGTTTTGTTTTGATTT
TTCGCACCGACATTTAAATGTTTTATATAATTGCAGGATGATGTTAAAAAGTGTATTCGA
ATGTTGGAAGACTCAACTCGTCTAGTGAATTTGAATGGAATGTTTAGCAAAAATGAATCG
CATGAAGAGATAGCCACAAATAATCTCAAATATTTGCTGCTGCCTTTTCTACTCGCACAA
TCGACTTTGAAATTAACTAATGTACAGGATCGCAAAAATGTCGTGGATGTTGCAAAAATA
TATTTCGATGATTTTCTCAAACGTTGTGAGGAATATGGATTATGTGAGAGAAGCACGACT
GCCGTTTCAAAAAATCAAGATATTATTTTACGCGATGAAATACAGAAATTAACTCAAATG
GCTCAACAAAGAAACCAAAAACTACAGAAATATCAACAGAAAAAGGAACTGAAGGATCAA
ATTAAACAACTTAAAATTGCAATGGAAAGGGATGATTCTGACGAAGACACAAAAAGAAAT
TTTTACTTGAAACTTATCAAATCATGCGTATGGGAGACACAAGATGAATTATCGACATTG
GAACAAGAGTGTGAAATTCTCGAACATATCGCGAAATTAAAGGAACATGACTCAGAAT
>g5974.t9 Gene=g5974 Length=179
MLEDSTRLVNLNGMFSKNESHEEIATNNLKYLLLPFLLAQSTLKLTNVQDRKNVVDVAKI
YFDDFLKRCEEYGLCERSTTAVSKNQDIILRDEIQKLTQMAQQRNQKLQKYQQKKELKDQ
IKQLKIAMERDDSDEDTKRNFYLKLIKSCVWETQDELSTLEQECEILEHIAKLKEHDSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5974.t9 | Coils | Coil | Coil | 94 | 134 | - |
| 4 | g5974.t9 | Gene3D | G3DSA:1.25.40.540 | - | 1 | 179 | 6.4E-51 |
| 2 | g5974.t9 | PANTHER | PTHR10933:SF9 | IMMUNOGLOBULIN (CD79A)-BINDING PROTEIN 1 | 2 | 176 | 2.3E-38 |
| 3 | g5974.t9 | PANTHER | PTHR10933 | IMMUNOGLOBULIN-BINDING PROTEIN 1 | 2 | 176 | 2.3E-38 |
| 1 | g5974.t9 | Pfam | PF04177 | TAP42-like family | 2 | 176 | 3.9E-45 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5974/g5974.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5974.t9.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.
