Gene loci information

Transcript annotation

  • This transcript has been annotated as Lissencephaly-1-like protein.

Parent gene

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.t4 TTS g1130.t4 8345485 8345485
chr_3 g1130 g1130.t4 isoform g1130.t4 8345864 8348551
chr_3 g1130 g1130.t4 exon g1130.t4.exon1 8345864 8346665
chr_3 g1130 g1130.t4 cds g1130.t4.CDS1 8345983 8346665
chr_3 g1130 g1130.t4 exon g1130.t4.exon2 8346756 8347213
chr_3 g1130 g1130.t4 cds g1130.t4.CDS2 8346756 8347213
chr_3 g1130 g1130.t4 exon g1130.t4.exon3 8348363 8348551
chr_3 g1130 g1130.t4 cds g1130.t4.CDS3 8348363 8348400
chr_3 g1130 g1130.t4 TSS g1130.t4 NA NA

Sequences

>g1130.t4 Gene=g1130 Length=1449
GAGTCGGATAGCCATAGTGTGACTCGATTCTTTGAATTTTAAAAAAGAGAGGAATTCTTT
GAGCTCCATTGAGCACATCGTTAATTTCAAGAGTAGTAGATACAAGAGAGGAATATAAAA
ATTGTACAAGATTCCATCATACGATCAAAAAATGAAAATGGTGTTGTCTCAGCGGCAGCG
CGAGGAGCTCAACCAAGCGATTGCTGATTATTTGGGTAGTAATGGTTATAACGATGCGCT
CGATGTTTTTCGGAAAGAGGCCGAAGTTCCAACAGAAATTGACCGAAAATATCGTGGATT
GTTGGAGAAAAAGTGGACTTCAGTCATTCGCTTACAGAAGAAAGTAATGGAATTGGAATC
AAAATTAAGCGAAGCCGAGAAGGAACTGATAGAAGGAGCACCGACAAAAGCCAAAAGAAC
GCCAACTGAATGGATTCCACGACAGCCAGAAAAATTCAAATTAACCGGTCATCGTGCGAC
TGTGAATCGGGTTATTTTTCATCCTGTTTTCAGCATGATGGTTTCAGCCAGCGAGGATGC
CACGATTAAAGTTTGGGATTTTGAAACGGGTGAATACGAAAGGACGCTTAAAGGACACAC
TGACTCAGTTCAGGATATAGCTTTTGATGCGCAAGGCAAATTGCTTGCCTCATGCAGTTC
AGATTTGTCAATAAAACTTTGGGACTTTCAGCAAACATTTGAATGTATTAAAACAATGCA
TGGTCATGATCATAATGTATCATCAGTTGCATTTGTGCCAGCTGGCGATTTTCTTCTATC
AGCATCACGTGACAAAACGATCAAGATGTGGGAAGTGGCGACTGGATATTGCGTGAAAAC
ATACACAGGCCATCGTGATTGGGTTAGAATGGTACGAATTAACTTTGACGGCACACTGAT
GGCAACATGTAGTAATGATCATTCGGTGCGTGTCTGGTGTATTAATTCCAAAGAATCGAA
AGTAGAATTACGTGAGCATGAACATACGGTTGAATGTCTTGCGTGGGCGCCAGAGTCAGC
TGCAGCATCGATCAATGAAGCAGCAGGTGCTGACAACAAAAAGGGTCAACATCAAGGGCC
ATTTTTAGCTTCTGGATCGCGCGATAAAACAATAAGGGTGTGGGATGTAACATCAGGCTT
GTGTTTGTTTACACTTTATGGTCATGACAATTGGGTGCGTGGAATCGTTTTTCATCCTGG
CGGTAAATATATGTTGACAGCTAGCGATGATAAAACAATACGCGTTTGGGATATTCGCAA
TAAACGTTGCTTAAAAGTTTTACAAGCCCATTCACATTTTTGTACTTCAATTGGTAAGTT
TAATCTATAAATAAATTTTTATAAGTAAAAATAACAATTTCTTTATTTTAATTAGATATG
CATAAATCTCATCCGTTTGTAATATCAGGAAGTGTCGATCAGACAGTCAAAGTCTACGAG
TGTCGTTAA

>g1130.t4 Gene=g1130 Length=392
MKMVLSQRQREELNQAIADYLGSNGYNDALDVFRKEAEVPTEIDRKYRGLLEKKWTSVIR
LQKKVMELESKLSEAEKELIEGAPTKAKRTPTEWIPRQPEKFKLTGHRATVNRVIFHPVF
SMMVSASEDATIKVWDFETGEYERTLKGHTDSVQDIAFDAQGKLLASCSSDLSIKLWDFQ
QTFECIKTMHGHDHNVSSVAFVPAGDFLLSASRDKTIKMWEVATGYCVKTYTGHRDWVRM
VRINFDGTLMATCSNDHSVRVWCINSKESKVELREHEHTVECLAWAPESAAASINEAAGA
DNKKGQHQGPFLASGSRDKTIRVWDVTSGLCLFTLYGHDNWVRGIVFHPGGKYMLTASDD
KTIRVWDIRNKRCLKVLQAHSHFCTSIGKFNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g1130.t4 CDD cd00200 WD40 104 387 6.88027E-100
18 g1130.t4 Coils Coil Coil 58 78 -
17 g1130.t4 Gene3D G3DSA:1.20.960.30 - 2 86 4.2E-32
16 g1130.t4 Gene3D G3DSA:2.130.10.10 - 101 391 6.4E-125
10 g1130.t4 Hamap MF_03141 Platelet-activating factor acetylhydrolase IB subunit alpha [PAFAH1B1]. 3 391 36.782524
8 g1130.t4 PANTHER PTHR44129 - 3 387 4.1E-203
9 g1130.t4 PANTHER PTHR44129:SF10 LISSENCEPHALY-1 HOMOLOG B 3 387 4.1E-203
19 g1130.t4 PIRSF PIRSF037647 LisH 1 391 1.7E-162
13 g1130.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 123 137 1.1E-9
11 g1130.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 312 326 1.1E-9
12 g1130.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 354 368 1.1E-9
1 g1130.t4 Pfam PF08513 LisH 11 37 1.2E-6
5 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 103 136 6.5E-4
6 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 142 178 2.8E-7
4 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 184 220 7.1E-8
3 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 226 262 1.0E-6
2 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 273 325 4.3E-5
7 g1130.t4 Pfam PF00400 WD domain, G-beta repeat 331 367 2.2E-9
30 g1130.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 123 137 -
32 g1130.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 165 179 -
31 g1130.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 208 222 -
28 g1130.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 312 326 -
29 g1130.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 354 368 -
40 g1130.t4 ProSiteProfiles PS50896 LIS1 homology (LisH) motif profile. 9 41 11.048
33 g1130.t4 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 104 376 64.356
35 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 104 145 16.323
37 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 146 180 14.786
34 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 189 230 16.758
39 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 231 272 12.547
38 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 309 334 10.876
36 g1130.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 335 376 17.259
21 g1130.t4 SMART SM00667 Lish 9 41 4.6E-7
23 g1130.t4 SMART SM00320 WD40_4 97 136 1.1E-6
27 g1130.t4 SMART SM00320 WD40_4 139 178 1.4E-10
24 g1130.t4 SMART SM00320 WD40_4 182 221 1.1E-10
25 g1130.t4 SMART SM00320 WD40_4 224 263 4.2E-9
26 g1130.t4 SMART SM00320 WD40_4 266 325 4.6E-7
22 g1130.t4 SMART SM00320 WD40_4 328 367 6.0E-12
14 g1130.t4 SUPERFAMILY SSF109925 Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain 4 76 3.66E-23
15 g1130.t4 SUPERFAMILY SSF50978 WD40 repeat-like 94 387 3.15E-91

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

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.

Raw TPM values