General information for g3125.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor ISY1-like protein.
Parent gene
- The parent gene g3125 is located on chr_3: 23076036..23076860 (- 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 | g3125 | g3125.t1 | TTS | g3125.t1 | 23076009 | 23076009 |
| chr_3 | g3125 | g3125.t1 | isoform | g3125.t1 | 23076036 | 23076860 |
| chr_3 | g3125 | g3125.t1 | exon | g3125.t1.exon1 | 23076036 | 23076444 |
| chr_3 | g3125 | g3125.t1 | cds | g3125.t1.CDS1 | 23076036 | 23076444 |
| chr_3 | g3125 | g3125.t1 | exon | g3125.t1.exon2 | 23076505 | 23076860 |
| chr_3 | g3125 | g3125.t1 | cds | g3125.t1.CDS2 | 23076505 | 23076860 |
| chr_3 | g3125 | g3125.t1 | TSS | g3125.t1 | 23076916 | 23076916 |
Sequences
>g3125.t1 Gene=g3125 Length=765
ATGGCAAGAAATGCTGAGAAGGCGATGACTACATTAGCTCGTTGGCGAGCAGCAAAAGAA
GCAGAAACGGGAAAAAATGAAAGAAGGCCATATCTTGCTAGCGAATGTACAGATGTAAAA
AAATGTGAAAAATGGAGAATTGAAATAATTCGTGAAATTTCAAAGAAAGTCGCTCAAATT
CAAAATGCTGGTCTCGGTGAGTTTCGAATACGTGATTTAAATGATGAAATCAATAAGTTA
TTGCGTGAGAAAAGACATTGGGAAAATCAAATATCGAATCTTGGCGGTCCGCATTATCGA
CGATATGGACCTAAAACGTTTGATGCTGAAGGAAGAGAAGTGCCTGGCAATCGAGGATAT
AAATATTTTGGCGCAGCTAAAGATTTGCCAGGCGTGAGAGAACTATTTGAGCAAGAACCA
CCTTCTGCGCCTAAGAAAACAAGAGTGGAGTTGATGAAAGATATTGATGCAAGTTATTAT
GGCTACTTAGATGACGACGATGGTGTTTTAATACCATTAGAAGAGAAAGCTTCAAAAGAA
GCAATGAAGAGATCAATGGAAGAGTGGAAGGAAAAATTGAAGAAGGGTGAAATTAAAACT
GGAGCTGAAGAGGATGATGATGATGATAGGTTGATTGATATGGATGTAAATGAGGAGTTG
TTAGCACCTCGATTTTCACATGTAGAAGTGCCAACTCAAAAAGACATTGAAGATGCATTG
TTAAGAAAAAAGAAAAGAGAATTGCTTGAAAAATATACTGAATAA
>g3125.t1 Gene=g3125 Length=254
MARNAEKAMTTLARWRAAKEAETGKNERRPYLASECTDVKKCEKWRIEIIREISKKVAQI
QNAGLGEFRIRDLNDEINKLLREKRHWENQISNLGGPHYRRYGPKTFDAEGREVPGNRGY
KYFGAAKDLPGVRELFEQEPPSAPKKTRVELMKDIDASYYGYLDDDDGVLIPLEEKASKE
AMKRSMEEWKEKLKKGEIKTGAEEDDDDDRLIDMDVNEELLAPRFSHVEVPTQKDIEDAL
LRKKKRELLEKYTE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3125.t1 | Coils | Coil | Coil | 70 | 90 | - |
| 6 | g3125.t1 | Coils | Coil | Coil | 179 | 199 | - |
| 5 | g3125.t1 | Gene3D | G3DSA:1.10.287.660 | Helix hairpin bin | 38 | 95 | 4.5E-29 |
| 4 | g3125.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 211 | - |
| 2 | g3125.t1 | PANTHER | PTHR13021 | PRE-MRNA-SPLICING FACTOR ISY1 | 1 | 253 | 8.4E-102 |
| 1 | g3125.t1 | Pfam | PF06246 | Isy1-like splicing family | 1 | 251 | 5.2E-95 |
| 3 | g3125.t1 | SUPERFAMILY | SSF140102 | ISY1 domain-like | 26 | 101 | 3.27E-31 |
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:0000350 | generation of catalytic spliceosome for second transesterification step | BP |
KEGG
Orthology
- This transcript has been annotated with K12870 (pre-mRNA-splicing factor ISY1)
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.
