General information for g1130.t1
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.t1 | TTS | g1130.t1 | 8345485 | 8345485 |
| chr_3 | g1130 | g1130.t1 | isoform | g1130.t1 | 8345864 | 8348394 |
| chr_3 | g1130 | g1130.t1 | exon | g1130.t1.exon1 | 8345864 | 8345937 |
| chr_3 | g1130 | g1130.t1 | cds | g1130.t1.CDS1 | 8345864 | 8345937 |
| chr_3 | g1130 | g1130.t1 | exon | g1130.t1.exon2 | 8346000 | 8346665 |
| chr_3 | g1130 | g1130.t1 | cds | g1130.t1.CDS2 | 8346000 | 8346665 |
| chr_3 | g1130 | g1130.t1 | exon | g1130.t1.exon3 | 8346756 | 8347213 |
| chr_3 | g1130 | g1130.t1 | cds | g1130.t1.CDS3 | 8346756 | 8347213 |
| chr_3 | g1130 | g1130.t1 | exon | g1130.t1.exon4 | 8348363 | 8348394 |
| chr_3 | g1130 | g1130.t1 | cds | g1130.t1.CDS4 | 8348363 | 8348394 |
| chr_3 | g1130 | g1130.t1 | TSS | g1130.t1 | NA | NA |
Sequences
>g1130.t1 Gene=g1130 Length=1230
ATGGTGTTGTCTCAGCGGCAGCGCGAGGAGCTCAACCAAGCGATTGCTGATTATTTGGGT
AGTAATGGTTATAACGATGCGCTCGATGTTTTTCGGAAAGAGGCCGAAGTTCCAACAGAA
ATTGACCGAAAATATCGTGGATTGTTGGAGAAAAAGTGGACTTCAGTCATTCGCTTACAG
AAGAAAGTAATGGAATTGGAATCAAAATTAAGCGAAGCCGAGAAGGAACTGATAGAAGGA
GCACCGACAAAAGCCAAAAGAACGCCAACTGAATGGATTCCACGACAGCCAGAAAAATTC
AAATTAACCGGTCATCGTGCGACTGTGAATCGGGTTATTTTTCATCCTGTTTTCAGCATG
ATGGTTTCAGCCAGCGAGGATGCCACGATTAAAGTTTGGGATTTTGAAACGGGTGAATAC
GAAAGGACGCTTAAAGGACACACTGACTCAGTTCAGGATATAGCTTTTGATGCGCAAGGC
AAATTGCTTGCCTCATGCAGTTCAGATTTGTCAATAAAACTTTGGGACTTTCAGCAAACA
TTTGAATGTATTAAAACAATGCATGGTCATGATCATAATGTATCATCAGTTGCATTTGTG
CCAGCTGGCGATTTTCTTCTATCAGCATCACGTGACAAAACGATCAAGATGTGGGAAGTG
GCGACTGGATATTGCGTGAAAACATACACAGGCCATCGTGATTGGGTTAGAATGGTACGA
ATTAACTTTGACGGCACACTGATGGCAACATGTAGTAATGATCATTCGGTGCGTGTCTGG
TGTATTAATTCCAAAGAATCGAAAGTAGAATTACGTGAGCATGAACATACGGTTGAATGT
CTTGCGTGGGCGCCAGAGTCAGCTGCAGCATCGATCAATGAAGCAGCAGGTGCTGACAAC
AAAAAGGGTCAACATCAAGGGCCATTTTTAGCTTCTGGATCGCGCGATAAAACAATAAGG
GTGTGGGATGTAACATCAGGCTTGTGTTTGTTTACACTTTATGGTCATGACAATTGGGTG
CGTGGAATCGTTTTTCATCCTGGCGGTAAATATATGTTGACAGCTAGCGATGATAAAACA
ATACGCGTTTGGGATATTCGCAATAAACGTTGCTTAAAAGTTTTACAAGCCCATTCACAT
TTTTGTACTTCAATTGATATGCATAAATCTCATCCGTTTGTAATATCAGGAAGTGTCGAT
CAGACAGTCAAAGTCTACGAGTGTCGTTAA
>g1130.t1 Gene=g1130 Length=409
MVLSQRQREELNQAIADYLGSNGYNDALDVFRKEAEVPTEIDRKYRGLLEKKWTSVIRLQ
KKVMELESKLSEAEKELIEGAPTKAKRTPTEWIPRQPEKFKLTGHRATVNRVIFHPVFSM
MVSASEDATIKVWDFETGEYERTLKGHTDSVQDIAFDAQGKLLASCSSDLSIKLWDFQQT
FECIKTMHGHDHNVSSVAFVPAGDFLLSASRDKTIKMWEVATGYCVKTYTGHRDWVRMVR
INFDGTLMATCSNDHSVRVWCINSKESKVELREHEHTVECLAWAPESAAASINEAAGADN
KKGQHQGPFLASGSRDKTIRVWDVTSGLCLFTLYGHDNWVRGIVFHPGGKYMLTASDDKT
IRVWDIRNKRCLKVLQAHSHFCTSIDMHKSHPFVISGSVDQTVKVYECR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g1130.t1 | CDD | cd00200 | WD40 | 102 | 407 | 1.67357E-107 |
| 19 | g1130.t1 | Coils | Coil | Coil | 56 | 76 | - |
| 18 | g1130.t1 | Gene3D | G3DSA:1.20.960.30 | - | 1 | 84 | 4.8E-32 |
| 17 | g1130.t1 | Gene3D | G3DSA:2.130.10.10 | - | 99 | 409 | 1.5E-134 |
| 11 | g1130.t1 | Hamap | MF_03141 | Platelet-activating factor acetylhydrolase IB subunit alpha [PAFAH1B1]. | 1 | 407 | 39.824085 |
| 9 | g1130.t1 | PANTHER | PTHR44129 | - | 1 | 409 | 6.2E-217 |
| 10 | g1130.t1 | PANTHER | PTHR44129:SF10 | LISSENCEPHALY-1 HOMOLOG B | 1 | 409 | 6.2E-217 |
| 20 | g1130.t1 | PIRSF | PIRSF037647 | LisH | 1 | 408 | 1.3E-166 |
| 12 | g1130.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 121 | 135 | 1.3E-9 |
| 13 | g1130.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 310 | 324 | 1.3E-9 |
| 14 | g1130.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 352 | 366 | 1.3E-9 |
| 1 | g1130.t1 | Pfam | PF08513 | LisH | 9 | 35 | 1.2E-6 |
| 8 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 101 | 134 | 6.8E-4 |
| 2 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 140 | 176 | 3.0E-7 |
| 4 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 182 | 218 | 7.5E-8 |
| 7 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 224 | 260 | 1.1E-6 |
| 6 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 271 | 323 | 4.6E-5 |
| 5 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 329 | 365 | 2.4E-9 |
| 3 | g1130.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 370 | 406 | 4.7E-5 |
| 30 | g1130.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 121 | 135 | - |
| 34 | g1130.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 163 | 177 | - |
| 32 | g1130.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 206 | 220 | - |
| 31 | g1130.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 310 | 324 | - |
| 33 | g1130.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 352 | 366 | - |
| 43 | g1130.t1 | ProSiteProfiles | PS50896 | LIS1 homology (LisH) motif profile. | 7 | 39 | 11.048 |
| 35 | g1130.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 102 | 409 | 71.474 |
| 41 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 102 | 143 | 16.323 |
| 39 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 144 | 178 | 14.786 |
| 42 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 187 | 228 | 16.758 |
| 40 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 229 | 270 | 12.547 |
| 37 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 307 | 332 | 10.876 |
| 38 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 333 | 374 | 17.259 |
| 36 | g1130.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 375 | 409 | 10.074 |
| 22 | g1130.t1 | SMART | SM00667 | Lish | 7 | 39 | 4.6E-7 |
| 25 | g1130.t1 | SMART | SM00320 | WD40_4 | 95 | 134 | 1.1E-6 |
| 27 | g1130.t1 | SMART | SM00320 | WD40_4 | 137 | 176 | 1.4E-10 |
| 24 | g1130.t1 | SMART | SM00320 | WD40_4 | 180 | 219 | 1.1E-10 |
| 23 | g1130.t1 | SMART | SM00320 | WD40_4 | 222 | 261 | 4.2E-9 |
| 26 | g1130.t1 | SMART | SM00320 | WD40_4 | 264 | 323 | 4.6E-7 |
| 28 | g1130.t1 | SMART | SM00320 | WD40_4 | 326 | 365 | 6.0E-12 |
| 29 | g1130.t1 | SMART | SM00320 | WD40_4 | 368 | 407 | 1.2E-6 |
| 15 | g1130.t1 | SUPERFAMILY | SSF109925 | Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain | 2 | 74 | 3.92E-23 |
| 16 | g1130.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 92 | 406 | 2.04E-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 transcript has been annotated with K16794 (platelet-activating factor acetylhydrolase IB subunit alpha)
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.
