General information for g4018.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine/arginine repetitive matrix protein 1.
Parent gene
- The parent gene g4018 is located on chr_3: 29545823..29546678 (- 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_3 | g4018 | g4018.t6 | isoform | g4018.t6 | 29545823 | 29546678 |
| chr_3 | g4018 | g4018.t6 | exon | g4018.t6.exon1 | 29545823 | 29546234 |
| chr_3 | g4018 | g4018.t6 | cds | g4018.t6.CDS1 | 29545823 | 29546234 |
| chr_3 | g4018 | g4018.t6 | exon | g4018.t6.exon2 | 29546296 | 29546534 |
| chr_3 | g4018 | g4018.t6 | cds | g4018.t6.CDS2 | 29546296 | 29546474 |
| chr_3 | g4018 | g4018.t6 | exon | g4018.t6.exon3 | 29546666 | 29546678 |
| chr_3 | g4018 | g4018.t6 | TSS | g4018.t6 | NA | NA |
| chr_3 | g4018 | g4018.t6 | TTS | g4018.t6 | NA | NA |
Sequences
>g4018.t6 Gene=g4018 Length=664
ATGTTTTCGGTATGGAACTAGTCTGAGTCAAGACACAAGATTTAGTGACAAAGAAAAGAA
ACTCCTCAAAGAAATGAAATTTGGTGATGTATTGCGTGAAAAGGTTGATATAACAAAGGT
AAAGTTAGATGTAATTCGACCATGGATTTCTCAGAAGATGACACAAATGATGAAGCTTGA
AGACGATGTATTAGAAGAATATGTTATTAATCAATTAGAAGAGATGAAAATTCCTGATCC
AAAAAAGATACAAATTTATTTGACCGGCTTCTTAGGCAGTAAAAATGCGAAAATATTTGT
TGAACAATTATGGGAATTGCTGCTTTCAGCACAAGAATCTGATATAGGTATTCCGAAAGA
AATGATTGAAAGCAAAAAGGATGAAATATTAAAAAGAGAACGGAAGCGTTCAAAAAGTCC
ATATTATCTTCAAAGAAGTTCATCCAGAGAACGTGATAGAGCTGAACGAGAAGAGAAAGA
AAAGATTCCAGAGAAAAAAACAGTTCCAGAAGAAGCAATTAAGAAAGCTAATGAAATAAA
AGAGCGAACTCAATTGAAAAATGAATTAAGTAAGCGAGAAAAAGCCAATGACAAGTCACG
CAGTGTTGAGCGTTCGAGGGCTAAATCGAAAGATCGGAATTCAGACGATAAAAGAAAGGT
ACAA
>g4018.t6 Gene=g4018 Length=197
MKFGDVLREKVDITKVKLDVIRPWISQKMTQMMKLEDDVLEEYVINQLEEMKIPDPKKIQ
IYLTGFLGSKNAKIFVEQLWELLLSAQESDIGIPKEMIESKKDEILKRERKRSKSPYYLQ
RSSSRERDRAEREEKEKIPEKKTVPEEAIKKANEIKERTQLKNELSKREKANDKSRSVER
SRAKSKDRNSDDKRKVQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4018.t6 | Coils | Coil | Coil | 149 | 169 | - |
| 5 | g4018.t6 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 1 | 108 | 3.9E-39 |
| 8 | g4018.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 112 | 197 | - |
| 2 | g4018.t6 | PANTHER | PTHR23148 | SERINE/ARGININE REGULATED NUCLEAR MATRIX PROTEIN | 1 | 190 | 1.8E-42 |
| 3 | g4018.t6 | PANTHER | PTHR23148:SF0 | SERINE/ARGININE REPETITIVE MATRIX PROTEIN 1 | 1 | 190 | 1.8E-42 |
| 1 | g4018.t6 | Pfam | PF01480 | PWI domain | 19 | 89 | 9.0E-27 |
| 9 | g4018.t6 | ProSiteProfiles | PS51025 | PWI domain profile. | 1 | 100 | 38.539 |
| 7 | g4018.t6 | SMART | SM00311 | pwi_2 | 13 | 89 | 5.9E-22 |
| 4 | g4018.t6 | SUPERFAMILY | SSF101233 | PWI domain | 1 | 107 | 3.4E-37 |
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:0006397 | mRNA processing | 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