General information for g1130.t3
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.t3 | isoform | g1130.t3 | 8345477 | 8347065 |
| chr_3 | g1130 | g1130.t3 | exon | g1130.t3.exon1 | 8345477 | 8345937 |
| chr_3 | g1130 | g1130.t3 | TTS | g1130.t3 | 8345485 | 8345485 |
| chr_3 | g1130 | g1130.t3 | cds | g1130.t3.CDS1 | 8345864 | 8345937 |
| chr_3 | g1130 | g1130.t3 | exon | g1130.t3.exon2 | 8346000 | 8346665 |
| chr_3 | g1130 | g1130.t3 | cds | g1130.t3.CDS2 | 8346000 | 8346665 |
| chr_3 | g1130 | g1130.t3 | exon | g1130.t3.exon3 | 8346756 | 8347065 |
| chr_3 | g1130 | g1130.t3 | cds | g1130.t3.CDS3 | 8346756 | 8347056 |
| chr_3 | g1130 | g1130.t3 | TSS | g1130.t3 | NA | NA |
Sequences
>g1130.t3 Gene=g1130 Length=1437
AAGAAAGTAATGGAATTGGAATCAAAATTAAGCGAAGCCGAGAAGGAACTGATAGAAGGA
GCACCGACAAAAGCCAAAAGAACGCCAACTGAATGGATTCCACGACAGCCAGAAAAATTC
AAATTAACCGGTCATCGTGCGACTGTGAATCGGGTTATTTTTCATCCTGTTTTCAGCATG
ATGGTTTCAGCCAGCGAGGATGCCACGATTAAAGTTTGGGATTTTGAAACGGGTGAATAC
GAAAGGACGCTTAAAGGACACACTGACTCAGTTCAGGATATAGCTTTTGATGCGCAAGGC
AAATTGCTTGCCTCATGCAGTTCAGATTTGTCAATAAAACTTTGGGACTTTCAGCAAACA
TTTGAATGTATTAAAACAATGCATGGTCATGATCATAATGTATCATCAGTTGCATTTGTG
CCAGCTGGCGATTTTCTTCTATCAGCATCACGTGACAAAACGATCAAGATGTGGGAAGTG
GCGACTGGATATTGCGTGAAAACATACACAGGCCATCGTGATTGGGTTAGAATGGTACGA
ATTAACTTTGACGGCACACTGATGGCAACATGTAGTAATGATCATTCGGTGCGTGTCTGG
TGTATTAATTCCAAAGAATCGAAAGTAGAATTACGTGAGCATGAACATACGGTTGAATGT
CTTGCGTGGGCGCCAGAGTCAGCTGCAGCATCGATCAATGAAGCAGCAGGTGCTGACAAC
AAAAAGGGTCAACATCAAGGGCCATTTTTAGCTTCTGGATCGCGCGATAAAACAATAAGG
GTGTGGGATGTAACATCAGGCTTGTGTTTGTTTACACTTTATGGTCATGACAATTGGGTG
CGTGGAATCGTTTTTCATCCTGGCGGTAAATATATGTTGACAGCTAGCGATGATAAAACA
ATACGCGTTTGGGATATTCGCAATAAACGTTGCTTAAAAGTTTTACAAGCCCATTCACAT
TTTTGTACTTCAATTGATATGCATAAATCTCATCCGTTTGTAATATCAGGAAGTGTCGAT
CAGACAGTCAAAGTCTACGAGTGTCGTTAAATCTAGTGAACAGAACAGGATAATAAGTTG
CGTATTTATTTCATATTTCAACAAAGATGTGTAAAACAAAAAAAATCCAGTTGTCCGGTA
CAGCAGTGAAGTCCAATTTATTATTTTCATAGTTAATTTTTAAGTTAGAACGATGATGGA
AACATTCACAACAATGCAACAACTGAAACAAGAATAATAATAAGTTTATACACACACACA
GAGGAGAATTTATTTTTTTAATTTCCATCCCATTCTTTCACTACCTACCTACTATGCTCT
ATTTTTTTGTAAAAGTACTTTTATATTAAAATATATCTTAATTTTGATCTAAAGTTTGTA
TTTTTTTCTACATAAAATATGAAATTCATATTACTGAATTTTTATTAGCAAAAAAAA
>g1130.t3 Gene=g1130 Length=346
MELESKLSEAEKELIEGAPTKAKRTPTEWIPRQPEKFKLTGHRATVNRVIFHPVFSMMVS
ASEDATIKVWDFETGEYERTLKGHTDSVQDIAFDAQGKLLASCSSDLSIKLWDFQQTFEC
IKTMHGHDHNVSSVAFVPAGDFLLSASRDKTIKMWEVATGYCVKTYTGHRDWVRMVRINF
DGTLMATCSNDHSVRVWCINSKESKVELREHEHTVECLAWAPESAAASINEAAGADNKKG
QHQGPFLASGSRDKTIRVWDVTSGLCLFTLYGHDNWVRGIVFHPGGKYMLTASDDKTIRV
WDIRNKRCLKVLQAHSHFCTSIDMHKSHPFVISGSVDQTVKVYECR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g1130.t3 | CDD | cd00200 | WD40 | 39 | 344 | 9.2061E-106 |
| 14 | g1130.t3 | Gene3D | G3DSA:2.130.10.10 | - | 36 | 346 | 8.5E-135 |
| 29 | g1130.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 30 | g1130.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 19 | - |
| 8 | g1130.t3 | PANTHER | PTHR44129 | - | 1 | 346 | 3.0E-183 |
| 9 | g1130.t3 | PANTHER | PTHR44129:SF10 | LISSENCEPHALY-1 HOMOLOG B | 1 | 346 | 3.0E-183 |
| 15 | g1130.t3 | PIRSF | PIRSF037647 | LisH | 1 | 345 | 4.8E-142 |
| 10 | g1130.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 58 | 72 | 8.2E-10 |
| 12 | g1130.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 247 | 261 | 8.2E-10 |
| 11 | g1130.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 289 | 303 | 8.2E-10 |
| 4 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 38 | 71 | 5.5E-4 |
| 7 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 77 | 113 | 2.4E-7 |
| 2 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 119 | 155 | 6.0E-8 |
| 5 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 161 | 197 | 8.5E-7 |
| 3 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 208 | 260 | 3.6E-5 |
| 1 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 266 | 302 | 1.9E-9 |
| 6 | g1130.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 307 | 343 | 3.8E-5 |
| 24 | g1130.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 58 | 72 | - |
| 28 | g1130.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 100 | 114 | - |
| 27 | g1130.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 143 | 157 | - |
| 26 | g1130.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 247 | 261 | - |
| 25 | g1130.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 289 | 303 | - |
| 31 | g1130.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 39 | 346 | 71.474 |
| 33 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 39 | 80 | 16.323 |
| 34 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 81 | 115 | 14.786 |
| 38 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 124 | 165 | 16.758 |
| 32 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 166 | 207 | 12.547 |
| 36 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 244 | 269 | 10.876 |
| 37 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 270 | 311 | 17.259 |
| 35 | g1130.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 312 | 346 | 10.074 |
| 22 | g1130.t3 | SMART | SM00320 | WD40_4 | 32 | 71 | 1.1E-6 |
| 19 | g1130.t3 | SMART | SM00320 | WD40_4 | 74 | 113 | 1.4E-10 |
| 23 | g1130.t3 | SMART | SM00320 | WD40_4 | 117 | 156 | 1.1E-10 |
| 21 | g1130.t3 | SMART | SM00320 | WD40_4 | 159 | 198 | 4.2E-9 |
| 20 | g1130.t3 | SMART | SM00320 | WD40_4 | 201 | 260 | 4.6E-7 |
| 18 | g1130.t3 | SMART | SM00320 | WD40_4 | 263 | 302 | 6.0E-12 |
| 17 | g1130.t3 | SMART | SM00320 | WD40_4 | 305 | 344 | 1.2E-6 |
| 13 | g1130.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 29 | 343 | 1.3E-97 |
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.
