General information for g4018.t4
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.t4 | TTS | g4018.t4 | 29544340 | 29544340 |
| chr_3 | g4018 | g4018.t4 | isoform | g4018.t4 | 29545268 | 29546678 |
| chr_3 | g4018 | g4018.t4 | exon | g4018.t4.exon1 | 29545268 | 29546234 |
| chr_3 | g4018 | g4018.t4 | cds | g4018.t4.CDS1 | 29545268 | 29546234 |
| chr_3 | g4018 | g4018.t4 | exon | g4018.t4.exon2 | 29546296 | 29546534 |
| chr_3 | g4018 | g4018.t4 | cds | g4018.t4.CDS2 | 29546296 | 29546534 |
| chr_3 | g4018 | g4018.t4 | exon | g4018.t4.exon3 | 29546670 | 29546678 |
| chr_3 | g4018 | g4018.t4 | cds | g4018.t4.CDS3 | 29546670 | 29546678 |
| chr_3 | g4018 | g4018.t4 | TSS | g4018.t4 | NA | NA |
Sequences
>g4018.t4 Gene=g4018 Length=1215
ATGTTTTCGGGAACTAGTCTGAGTCAAGACACAAGATTTAGTGACAAAGAAAAGAAACTC
CTCAAAGAAATGAAATTTGGTGATGTATTGCGTGAAAAGGTTGATATAACAAAGGTAAAG
TTAGATGTAATTCGACCATGGATTTCTCAGAAGATGACACAAATGATGAAGCTTGAAGAC
GATGTATTAGAAGAATATGTTATTAATCAATTAGAAGAGATGAAAATTCCTGATCCAAAA
AAGATACAAATTTATTTGACCGGCTTCTTAGGCAGTAAAAATGCGAAAATATTTGTTGAA
CAATTATGGGAATTGCTGCTTTCAGCACAAGAATCTGATATAGGTATTCCGAAAGAAATG
ATTGAAAGCAAAAAGGATGAAATATTAAAAAGAGAACGGAAGCGTTCAAAAAGTCCATAT
TATCTTCAAAGAAGTTCATCCAGAGAACGTGATAGAGCTGAACGAGAAGAGAAAGAAAAG
ATTCCAGAGAAAAAAACAGTTCCAGAAGAAGCAATTAAGAAAGCTAATGAAATAAAAGAG
CGAACTCAATTGAAAAATGAATTAAGTAAGCGAGAAAAAGCCAATGACAAGTCACGCAGT
GTTGAGCGTTCGAGGGCTAAATCGAAAGATCGGAATTCAGACGATAAAAGAAAGGTACAA
AGAGACAGATCACGAGATCGACGAAGGTCACGTTCATATGATAGGACAAAAGATAGACGA
AGTCGAAGAAGCAGATCAAGACGCAAAAGTTATTCAAGAGAGAGACGAAGAAGTGTTTCA
CGTCGCAGACGAAGTCGATCCCGAAGAAGCCGTTCACACGATAGACGTGATCGTGATAGA
AATGATGCAAAGTCCAGAAAATCACCTGTCAAACGCAATCGAAGACGAGATCAATCGGTA
TCACTTTCAAGATCGAAGAGCAAAGAAAGACTGTCGAAAACACAAAAGAAACTTCTTGAA
TTTGCTAAAAACAATACCAAGACAACAAAAAAATCACGTTCACGTAGTCAATCAGCAAAA
TCTTCGTCTCGGAGTCCACCTAATAAGAAACGGCGTCAAAGTTCGAGTGCAAGCAGAAGC
AGCAGTTCACCAGAACGACAAAAGCGCAATGATAACAACTCCTCTAGCAAAGTTCGTCAA
TATCGTTCAAAGCGAAAATCCGATAGTGAATCAGAAGATGAGCGAATGAGAGAACGAAAC
AATCAGCACCAACGA
>g4018.t4 Gene=g4018 Length=405
MFSGTSLSQDTRFSDKEKKLLKEMKFGDVLREKVDITKVKLDVIRPWISQKMTQMMKLED
DVLEEYVINQLEEMKIPDPKKIQIYLTGFLGSKNAKIFVEQLWELLLSAQESDIGIPKEM
IESKKDEILKRERKRSKSPYYLQRSSSRERDRAEREEKEKIPEKKTVPEEAIKKANEIKE
RTQLKNELSKREKANDKSRSVERSRAKSKDRNSDDKRKVQRDRSRDRRRSRSYDRTKDRR
SRRSRSRRKSYSRERRRSVSRRRRSRSRRSRSHDRRDRDRNDAKSRKSPVKRNRRRDQSV
SLSRSKSKERLSKTQKKLLEFAKNNTKTTKKSRSRSQSAKSSSRSPPNKKRRQSSSASRS
SSSPERQKRNDNNSSSKVRQYRSKRKSDSESEDERMRERNNQHQR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4018.t4 | Coils | Coil | Coil | 172 | 192 | - |
| 5 | g4018.t4 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 21 | 131 | 1.0E-38 |
| 8 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 405 | - |
| 9 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 239 | - |
| 13 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 271 | - |
| 10 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 286 | - |
| 11 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 294 | 317 | - |
| 12 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 335 | 363 | - |
| 14 | g4018.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 405 | - |
| 2 | g4018.t4 | PANTHER | PTHR23148 | SERINE/ARGININE REGULATED NUCLEAR MATRIX PROTEIN | 2 | 402 | 8.6E-66 |
| 3 | g4018.t4 | PANTHER | PTHR23148:SF0 | SERINE/ARGININE REPETITIVE MATRIX PROTEIN 1 | 2 | 402 | 8.6E-66 |
| 1 | g4018.t4 | Pfam | PF01480 | PWI domain | 42 | 112 | 3.4E-26 |
| 15 | g4018.t4 | ProSiteProfiles | PS51025 | PWI domain profile. | 23 | 123 | 36.896 |
| 7 | g4018.t4 | SMART | SM00311 | pwi_2 | 36 | 112 | 5.9E-22 |
| 4 | g4018.t4 | SUPERFAMILY | SSF101233 | PWI domain | 21 | 130 | 2.35E-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 transcript has been annotated with K13171 (serine/arginine repetitive matrix protein 1)
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.
