General information for g3124.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g3124.t1 | 23072356 | 23072356 |
| chr_3 | g3124 | g3124.t1 | isoform | g3124.t1 | 23072407 | 23075860 |
| chr_3 | g3124 | g3124.t1 | exon | g3124.t1.exon1 | 23072407 | 23074318 |
| chr_3 | g3124 | g3124.t1 | cds | g3124.t1.CDS1 | 23072407 | 23074318 |
| chr_3 | g3124 | g3124.t1 | exon | g3124.t1.exon2 | 23074646 | 23075146 |
| chr_3 | g3124 | g3124.t1 | cds | g3124.t1.CDS2 | 23074646 | 23075146 |
| chr_3 | g3124 | g3124.t1 | exon | g3124.t1.exon3 | 23075294 | 23075399 |
| chr_3 | g3124 | g3124.t1 | cds | g3124.t1.CDS3 | 23075294 | 23075399 |
| chr_3 | g3124 | g3124.t1 | exon | g3124.t1.exon4 | 23075842 | 23075860 |
| chr_3 | g3124 | g3124.t1 | cds | g3124.t1.CDS4 | 23075842 | 23075860 |
| chr_3 | g3124 | g3124.t1 | TSS | g3124.t1 | 23075916 | 23075916 |
Sequences
>g3124.t1 Gene=g3124 Length=2538
ATGGATATTTTAAATCGAGATGACTCCAAGGAGGATGAAATTTCGTGTGCATCTTGTTTG
AATAGCTTAGAAAATGAGGAATTTATTACGGCATTGGGACAAAACTATCACATCGACTGC
TTTCGCTGTTCGGTATGTGACAGGGAAATGTGGAACACGAATTTTTACTTTGAAAAGGAT
GGACTGCTTTTTTGCAAAGATGATTATTGGCAAAAATTTGGGGAGTGTTGTCAAGAATGT
GGTGAAGTAGTGAGTGGACCGATTATGATTGCGGGTGATCATCGTTTTCATCCTGAATGT
TTTTGTTGTAAAATTTGTAAAAATGTAATTGGTGATGGTGACTCTTATGCATTAATTGAT
CGTACGAATCTTTTCTGTGGTTCGTGTCATCGACGACAAATGCCATCATCACAAATTCAA
CAAAAATATAGCACTAATGAACCAGCCTCAATGACTGTCACAATCATCAAGAAACCGCCT
CATTCTATCAGATTGGTCGAAATTCCTTGGAAGAGTGAAAATAAAAATTCCATTCGTTTA
TCTATAGACGAAGAGGCTGCAATGATGAGTCCCCCTTCCAATACTTCATCATCAACAACA
CGATGTCGTGGAGTGAGAATTTCAGAATTGGATGAAAATCCGGATTTAATGGCATTGCAT
GTCGGTGATAGAATCATTGATATAAATGGACATTCAGTTGATGGAAAAAATTCAATTAAT
GATCTTCATAAAATTATCGATGACACTGATCGAGTACTTCAACTTACAATAGAACACGAG
CCAAATACTATAACAAGACGAAATCCAATTTCAGGAGAATTAGAATTTCTAACGACTCAA
ACAGTTAGTAGAAATGCCTCATCGTCATCAATATGTCCTACAAATGATTCGACTTTGATG
TTACCGCCAGTTCCTAAATTGGATAAAGCTCGAATTGCGACTAGAATGGACGAGGGATAT
ATGAGCGGTACACCAAAGAAATTTAATAAGCTTACACGTAATCAAAAAGGCAACCAGAAA
AGAACAACGAAATTCAATTGTGAACAGTCAACAAATTCACTAAGAGATGGTAAAGAAAGA
AGTAGTAGCATGAGTAAATTGATGCTAGGTCATAATGTAAATACAACCGATGGCCATAAT
CAAATGTTTGATCTGTCACGAACAAAAAGTTTTCGTGTTGAGCCGCAAAATGGTGTTCAT
AATCATAGAATTTTCCGAGCATCAGATTTAGTCATTGGTGAAATGCTAGGAAGAGGATTT
TTTGGTGAAGTTTATAAGGTAACTCATAAGGAAACAAAAGAAGTCATGGTTTTGAAAGAA
CTTTATAAATGGGTTGATGATGATGCACAGCGAAATTTTCTTAAAGAAGTTGCCGTCCTT
CGTTCACTTAATCATCGTAACGTTCTTCGATTTATTGGTGTTCTGTACAAAGAGAAGAAA
CTTCATCTTATTACTGAGTTTATAAGTGGAGGAACTTTAGCTTCGTTACTTCATGGTGCC
TCAAATCACATTCCACTTTCATGGAGTGAAAGAATTCATTTTGCTCGTGACATTAGTATG
GGCATGAGTTATTTGCATTCAATGAATATTATTCATCGAGATTTAAATTCAGGGAATTGT
CTCGTACGTGATGTCGGTAAAGATAGAACTGTAATTGTGGCCGATTTTGGTTTAGCAAGA
TTATGCAAAGCAGCGACAGATAGCGGAACTGGAACTGTGATAAATCGCAAAAGTCAGCGT
GAAAGACGTAAACGTTATACTGTGGTTGGCACGCCGTGGTATATGGCACCAGAGATGTTA
AGAGGCAACAAATATGATGAAAAGGTCGATGTTTTTTCATTTGGCATCATTATGTGTGAA
CTTATAAGTAGACTACAAGCAGATCCCGACTACATGCCAAGAACTGACGATTTTGGATTG
AATCGTCTCGAATTTATTGAGTTGTGTAAATCTCAAAATGATCCATGTCCAGAAGTGTTG
TACAAAATTGCTTTTCTTTGCTGCGATCTTAATCCTGATCGACGGCCCTCATTCAAAACG
TTACAAGAATGGTTTGATCGCATTACTGTTCATTGTGCCATAATTGGAAGTTTTCATAGT
CAACTGCCATCAGATCTCATTAATGAAATAAATAATTTTCATGGTGAAGAGACTTCAACA
TGTAATACACCTGATATATCAAATAGTAAAGAAATCCCACCTACATTCACCATCATACAA
CAACAACAGCAACTCATCGAGACGTCAAATACAAAAGATGAAATTGATTCGTTACAAACG
TCATCGTCACCATCGGAAAAGAAAAAAGAAGTGCCTGAACTTATTGCTCGTACAATGTCG
CCACATTTAGCAAAAGAATTTACTGCAAATGGTGATAGAGTTCGCGATTCATGGAGAGCA
CGACGAAAACAAAAAATTCGCGACAATCGTCAACAACGTGTGAAGAAGGACGTTCACACA
AATAACAACAATACAAATAATGTGGTTGAATCGATTCATAAGAAACCATCGCCATCAACG
ACTGTAACAAACACGTGA
>g3124.t1 Gene=g3124 Length=845
MDILNRDDSKEDEISCASCLNSLENEEFITALGQNYHIDCFRCSVCDREMWNTNFYFEKD
GLLFCKDDYWQKFGECCQECGEVVSGPIMIAGDHRFHPECFCCKICKNVIGDGDSYALID
RTNLFCGSCHRRQMPSSQIQQKYSTNEPASMTVTIIKKPPHSIRLVEIPWKSENKNSIRL
SIDEEAAMMSPPSNTSSSTTRCRGVRISELDENPDLMALHVGDRIIDINGHSVDGKNSIN
DLHKIIDDTDRVLQLTIEHEPNTITRRNPISGELEFLTTQTVSRNASSSSICPTNDSTLM
LPPVPKLDKARIATRMDEGYMSGTPKKFNKLTRNQKGNQKRTTKFNCEQSTNSLRDGKER
SSSMSKLMLGHNVNTTDGHNQMFDLSRTKSFRVEPQNGVHNHRIFRASDLVIGEMLGRGF
FGEVYKVTHKETKEVMVLKELYKWVDDDAQRNFLKEVAVLRSLNHRNVLRFIGVLYKEKK
LHLITEFISGGTLASLLHGASNHIPLSWSERIHFARDISMGMSYLHSMNIIHRDLNSGNC
LVRDVGKDRTVIVADFGLARLCKAATDSGTGTVINRKSQRERRKRYTVVGTPWYMAPEML
RGNKYDEKVDVFSFGIIMCELISRLQADPDYMPRTDDFGLNRLEFIELCKSQNDPCPEVL
YKIAFLCCDLNPDRRPSFKTLQEWFDRITVHCAIIGSFHSQLPSDLINEINNFHGEETST
CNTPDISNSKEIPPTFTIIQQQQQLIETSNTKDEIDSLQTSSSPSEKKKEVPELIARTMS
PHLAKEFTANGDRVRDSWRARRKQKIRDNRQQRVKKDVHTNNNNTNNVVESIHKKPSPST
TVTNT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g3124.t1 | CDD | cd09365 | LIM2_LIMK | 77 | 130 | 2.65799E-26 |
| 13 | g3124.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 5 | 75 | 5.5E-16 |
| 14 | g3124.t1 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 76 | 134 | 4.9E-13 |
| 12 | g3124.t1 | Gene3D | G3DSA:2.30.42.10 | - | 152 | 268 | 8.1E-22 |
| 10 | g3124.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 399 | 487 | 1.1E-30 |
| 11 | g3124.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 488 | 699 | 2.7E-54 |
| 23 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 334 | 352 | - |
| 25 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 334 | 363 | - |
| 22 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 751 | 765 | - |
| 24 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 751 | 771 | - |
| 21 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 845 | - |
| 26 | g3124.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 818 | 845 | - |
| 4 | g3124.t1 | PANTHER | PTHR46485:SF4 | LIM DOMAIN KINASE 1 | 14 | 832 | 2.4E-241 |
| 5 | g3124.t1 | PANTHER | PTHR46485 | LIM DOMAIN KINASE 1 | 14 | 832 | 2.4E-241 |
| 2 | g3124.t1 | Pfam | PF00412 | LIM domain | 16 | 73 | 1.4E-13 |
| 3 | g3124.t1 | Pfam | PF00412 | LIM domain | 77 | 132 | 2.5E-9 |
| 1 | g3124.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 411 | 683 | 6.2E-52 |
| 16 | g3124.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 16 | 50 | - |
| 17 | g3124.t1 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 77 | 110 | - |
| 18 | g3124.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 416 | 439 | - |
| 28 | g3124.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 14 | 75 | 14.157 |
| 27 | g3124.t1 | ProSiteProfiles | PS50023 | LIM domain profile. | 77 | 136 | 8.851 |
| 29 | g3124.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 165 | 261 | 8.506 |
| 30 | g3124.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 410 | 685 | 39.835 |
| 20 | g3124.t1 | SMART | SM00132 | lim_4 | 15 | 68 | 1.6E-13 |
| 19 | g3124.t1 | SMART | SM00132 | lim_4 | 76 | 129 | 7.3E-9 |
| 7 | g3124.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 42 | 107 | 8.99E-14 |
| 8 | g3124.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 101 | 133 | 1.15E-8 |
| 6 | g3124.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 203 | 266 | 2.23E-6 |
| 9 | g3124.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 403 | 704 | 2.02E-73 |
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:0005524 | ATP binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K05743 (LIM domain kinase 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.
