General information for g3124.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative LIM domain kinase 1.
Parent gene
- The parent gene g3124 is located on chr_3: 23073698..23075860 (- 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 | g3124 | g3124.t2 | TTS | g3124.t2 | 23072356 | 23072356 |
| chr_3 | g3124 | g3124.t2 | isoform | g3124.t2 | 23072407 | 23073144 |
| chr_3 | g3124 | g3124.t2 | exon | g3124.t2.exon1 | 23072407 | 23073144 |
| chr_3 | g3124 | g3124.t2 | cds | g3124.t2.CDS1 | 23072407 | 23073093 |
| chr_3 | g3124 | g3124.t2 | TSS | g3124.t2 | NA | NA |
Sequences
>g3124.t2 Gene=g3124 Length=738
AGAGGCAACAAATATGATGAAAAGGTCGATGTTTTTTCATTTGGCATCATTATGTGTGAA
CTTATAAGTAGACTACAAGCAGATCCCGACTACATGCCAAGAACTGACGATTTTGGATTG
AATCGTCTCGAATTTATTGAGTTGTGTAAATCTCAAAATGATCCATGTCCAGAAGTGTTG
TACAAAATTGCTTTTCTTTGCTGCGATCTTAATCCTGATCGACGGCCCTCATTCAAAACG
TTACAAGAATGGTTTGATCGCATTACTGTTCATTGTGCCATAATTGGAAGTTTTCATAGT
CAACTGCCATCAGATCTCATTAATGAAATAAATAATTTTCATGGTGAAGAGACTTCAACA
TGTAATACACCTGATATATCAAATAGTAAAGAAATCCCACCTACATTCACCATCATACAA
CAACAACAGCAACTCATCGAGACGTCAAATACAAAAGATGAAATTGATTCGTTACAAACG
TCATCGTCACCATCGGAAAAGAAAAAAGAAGTGCCTGAACTTATTGCTCGTACAATGTCG
CCACATTTAGCAAAAGAATTTACTGCAAATGGTGATAGAGTTCGCGATTCATGGAGAGCA
CGACGAAAACAAAAAATTCGCGACAATCGTCAACAACGTGTGAAGAAGGACGTTCACACA
AATAACAACAATACAAATAATGTGGTTGAATCGATTCATAAGAAACCATCGCCATCAACG
ACTGTAACAAACACGTGA
>g3124.t2 Gene=g3124 Length=228
MCELISRLQADPDYMPRTDDFGLNRLEFIELCKSQNDPCPEVLYKIAFLCCDLNPDRRPS
FKTLQEWFDRITVHCAIIGSFHSQLPSDLINEINNFHGEETSTCNTPDISNSKEIPPTFT
IIQQQQQLIETSNTKDEIDSLQTSSSPSEKKKEVPELIARTMSPHLAKEFTANGDRVRDS
WRARRKQKIRDNRQQRVKKDVHTNNNNTNNVVESIHKKPSPSTTVTNT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3124.t2 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 1 | 84 | 1.9E-7 |
| 4 | g3124.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 134 | 148 | - |
| 5 | g3124.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 134 | 154 | - |
| 3 | g3124.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 183 | 228 | - |
| 6 | g3124.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 228 | - |
| 1 | g3124.t2 | PANTHER | PTHR46485:SF4 | LIM DOMAIN KINASE 1 | 1 | 215 | 1.5E-31 |
| 2 | g3124.t2 | PANTHER | PTHR46485 | LIM DOMAIN KINASE 1 | 1 | 215 | 1.5E-31 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
