General information for g1130.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lissencephaly-1-like protein.
Parent gene
- The parent gene g1130 is located on chr_3: 8345864..8348551 (- 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 | g1130 | g1130.t2 | isoform | g1130.t2 | 8345477 | 8346665 |
| chr_3 | g1130 | g1130.t2 | exon | g1130.t2.exon1 | 8345477 | 8345937 |
| chr_3 | g1130 | g1130.t2 | TTS | g1130.t2 | 8345485 | 8345485 |
| chr_3 | g1130 | g1130.t2 | cds | g1130.t2.CDS1 | 8345864 | 8345937 |
| chr_3 | g1130 | g1130.t2 | exon | g1130.t2.exon2 | 8346000 | 8346665 |
| chr_3 | g1130 | g1130.t2 | cds | g1130.t2.CDS2 | 8346000 | 8346597 |
| chr_3 | g1130 | g1130.t2 | TSS | g1130.t2 | NA | NA |
Sequences
>g1130.t2 Gene=g1130 Length=1127
CCTCATGCAGTTCAGATTTGTCAATAAAACTTTGGGACTTTCAGCAAACATTTGAATGTA
TTAAAACAATGCATGGTCATGATCATAATGTATCATCAGTTGCATTTGTGCCAGCTGGCG
ATTTTCTTCTATCAGCATCACGTGACAAAACGATCAAGATGTGGGAAGTGGCGACTGGAT
ATTGCGTGAAAACATACACAGGCCATCGTGATTGGGTTAGAATGGTACGAATTAACTTTG
ACGGCACACTGATGGCAACATGTAGTAATGATCATTCGGTGCGTGTCTGGTGTATTAATT
CCAAAGAATCGAAAGTAGAATTACGTGAGCATGAACATACGGTTGAATGTCTTGCGTGGG
CGCCAGAGTCAGCTGCAGCATCGATCAATGAAGCAGCAGGTGCTGACAACAAAAAGGGTC
AACATCAAGGGCCATTTTTAGCTTCTGGATCGCGCGATAAAACAATAAGGGTGTGGGATG
TAACATCAGGCTTGTGTTTGTTTACACTTTATGGTCATGACAATTGGGTGCGTGGAATCG
TTTTTCATCCTGGCGGTAAATATATGTTGACAGCTAGCGATGATAAAACAATACGCGTTT
GGGATATTCGCAATAAACGTTGCTTAAAAGTTTTACAAGCCCATTCACATTTTTGTACTT
CAATTGATATGCATAAATCTCATCCGTTTGTAATATCAGGAAGTGTCGATCAGACAGTCA
AAGTCTACGAGTGTCGTTAAATCTAGTGAACAGAACAGGATAATAAGTTGCGTATTTATT
TCATATTTCAACAAAGATGTGTAAAACAAAAAAAATCCAGTTGTCCGGTACAGCAGTGAA
GTCCAATTTATTATTTTCATAGTTAATTTTTAAGTTAGAACGATGATGGAAACATTCACA
ACAATGCAACAACTGAAACAAGAATAATAATAAGTTTATACACACACACAGAGGAGAATT
TATTTTTTTAATTTCCATCCCATTCTTTCACTACCTACCTACTATGCTCTATTTTTTTGT
AAAAGTACTTTTATATTAAAATATATCTTAATTTTGATCTAAAGTTTGTATTTTTTTCTA
CATAAAATATGAAATTCATATTACTGAATTTTTATTAGCAAAAAAAA
>g1130.t2 Gene=g1130 Length=223
MHGHDHNVSSVAFVPAGDFLLSASRDKTIKMWEVATGYCVKTYTGHRDWVRMVRINFDGT
LMATCSNDHSVRVWCINSKESKVELREHEHTVECLAWAPESAAASINEAAGADNKKGQHQ
GPFLASGSRDKTIRVWDVTSGLCLFTLYGHDNWVRGIVFHPGGKYMLTASDDKTIRVWDI
RNKRCLKVLQAHSHFCTSIDMHKSHPFVISGSVDQTVKVYECR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g1130.t2 | CDD | cd00200 | WD40 | 1 | 221 | 2.78048E-66 |
| 12 | g1130.t2 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 223 | 1.3E-94 |
| 6 | g1130.t2 | PANTHER | PTHR44129 | - | 1 | 223 | 3.2E-114 |
| 7 | g1130.t2 | PANTHER | PTHR44129:SF10 | LISSENCEPHALY-1 HOMOLOG B | 1 | 223 | 3.2E-114 |
| 10 | g1130.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 20 | 34 | 5.3E-10 |
| 9 | g1130.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 124 | 138 | 5.3E-10 |
| 8 | g1130.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 166 | 180 | 5.3E-10 |
| 4 | g1130.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 2 | 32 | 3.2E-6 |
| 5 | g1130.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 38 | 74 | 4.5E-7 |
| 3 | g1130.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 85 | 137 | 1.7E-5 |
| 2 | g1130.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 143 | 179 | 9.8E-10 |
| 1 | g1130.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 184 | 220 | 2.0E-5 |
| 16 | g1130.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 20 | 34 | - |
| 15 | g1130.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 124 | 138 | - |
| 14 | g1130.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 166 | 180 | - |
| 22 | g1130.t2 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 223 | 49.883 |
| 26 | g1130.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 1 | 42 | 16.758 |
| 27 | g1130.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 43 | 84 | 12.547 |
| 24 | g1130.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 121 | 146 | 10.876 |
| 23 | g1130.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 147 | 188 | 17.259 |
| 25 | g1130.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 189 | 223 | 10.074 |
| 20 | g1130.t2 | SMART | SM00320 | WD40_4 | 1 | 33 | 0.027 |
| 18 | g1130.t2 | SMART | SM00320 | WD40_4 | 36 | 75 | 4.2E-9 |
| 21 | g1130.t2 | SMART | SM00320 | WD40_4 | 78 | 137 | 4.6E-7 |
| 17 | g1130.t2 | SMART | SM00320 | WD40_4 | 140 | 179 | 6.0E-12 |
| 19 | g1130.t2 | SMART | SM00320 | WD40_4 | 182 | 221 | 1.2E-6 |
| 11 | g1130.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 2 | 220 | 1.1E-65 |
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.
