General information for g10583.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor syf1-like protein.
Parent gene
- The parent gene g10583 is located on chr_1: 10529911..10530557 (+ 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_1 | g10583 | g10583.t2 | isoform | g10583.t2 | 10529911 | 10530557 |
| chr_1 | g10583 | g10583.t2 | exon | g10583.t2.exon1 | 10529911 | 10530557 |
| chr_1 | g10583 | g10583.t2 | cds | g10583.t2.CDS1 | 10529949 | 10530557 |
| chr_1 | g10583 | g10583.t2 | TTS | g10583.t2 | 10530604 | 10530604 |
| chr_1 | g10583 | g10583.t2 | TSS | g10583.t2 | NA | NA |
Sequences
>g10583.t2 Gene=g10583 Length=647
TTCCACGAACAAGACCTATTTATGAAAAAGCTATTGAAATGTTGCCTGAAACAAAAGCAC
GTGAAATGTGCATTCGATTTGCAGAGATGGAAACAAAACTTGGAGAAATTGATAGAGCGC
GTGTTATTTATTCACATTGCAGTCAAATGTGTGATCCTCGAATCACTCAAGATTTTTGGC
AAAAATGGAAAGATTTTGAAATTCGTCATGGTAATGAAGAAACGATGAGAGAAATGTTGA
GAATTAAACGAAGCGTACAAGCAACTTATAACACTCAAGTTAACATGATGTCCGCACAAA
TACCATCATCAATTGAACCGGTAAAAAGTGCAATGCAAGCGCTTGAAGCGAAAGCAATCG
AGACAAATTATAAACAAAATTTGGTATCTGCCGCTGTCGGTGCAAATATTGCATTTGTAC
GAGGAGAAGTTCAGGGAGGTGATTATAAGAAGAAGCAACAAGATGATGGTGCAGTTTATA
ATCCAGATGAAATTGACATTGATATGGATGACGACAATAGTGAGGAATCTGATGAGGAAA
ATGATACAGAAGAAGGAAAAGAATTGAAGAATATACCAATTGAGAAGCAACCAGTTCCTG
CGACCGTTTTTGGTGGACTGAAAAAAAAAGATTCGGATTCTGAATAA
>g10583.t2 Gene=g10583 Length=202
MLPETKAREMCIRFAEMETKLGEIDRARVIYSHCSQMCDPRITQDFWQKWKDFEIRHGNE
ETMREMLRIKRSVQATYNTQVNMMSAQIPSSIEPVKSAMQALEAKAIETNYKQNLVSAAV
GANIAFVRGEVQGGDYKKKQQDDGAVYNPDEIDIDMDDDNSEESDEENDTEEGKELKNIP
IEKQPVPATVFGGLKKKDSDSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10583.t2 | Gene3D | G3DSA:1.25.40.10 | - | 3 | 111 | 1.2E-11 |
| 4 | g10583.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 135 | 202 | - |
| 5 | g10583.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 148 | 170 | - |
| 1 | g10583.t2 | PANTHER | PTHR11246:SF5 | PRE-MRNA-SPLICING FACTOR SYF1 | 2 | 154 | 2.2E-41 |
| 2 | g10583.t2 | PANTHER | PTHR11246 | PRE-MRNA SPLICING FACTOR | 2 | 154 | 2.2E-41 |
| 3 | g10583.t2 | SUPERFAMILY | SSF48452 | TPR-like | 7 | 68 | 7.96E-11 |
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:0005515 | protein binding | MF |
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.
