Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein LST8-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_4 g17274 g17274.t3 TSS g17274.t3 13005226 13005226
chr_4 g17274 g17274.t3 isoform g17274.t3 13005321 13006689
chr_4 g17274 g17274.t3 exon g17274.t3.exon1 13005321 13005437
chr_4 g17274 g17274.t3 cds g17274.t3.CDS1 13005321 13005437
chr_4 g17274 g17274.t3 exon g17274.t3.exon2 13005568 13005752
chr_4 g17274 g17274.t3 cds g17274.t3.CDS2 13005568 13005752
chr_4 g17274 g17274.t3 exon g17274.t3.exon3 13006053 13006453
chr_4 g17274 g17274.t3 cds g17274.t3.CDS3 13006053 13006453
chr_4 g17274 g17274.t3 exon g17274.t3.exon4 13006545 13006689
chr_4 g17274 g17274.t3 cds g17274.t3.CDS4 13006545 13006645
chr_4 g17274 g17274.t3 TTS g17274.t3 13006711 13006711

Sequences

>g17274.t3 Gene=g17274 Length=848
ATGGTTCAAACAGAAGGTGATCCAATTTTAGCAACTGGTGGTTATGACCATACTATAAAA
ATTTGGGCACCTTACTCAGGAACATCAATTAAAACTCTTCAACATTCTGATTCACAAGTA
AATGCACTAGTAATAAAAAATTATTTAGCTGCCGGTGGATTTCAATCAATTCGTCTCTAT
GATTTGAATGCAAGTACAAATCCATTAATTAATTTTGAAGGTGTCAGTAAAAATGTCACA
TCAGTTGGATTTCAAGAAGATGGAAGATTTATGTACACTGGATCAGAAGATTGCAGAGTT
CGTATCTGGGACCTAAATTGTCCACAACCAGTTTGTAAGCGAATGTTTGACTGCCTTACT
CCAGTTGCATCAGTTTGTCTTCATCCAAATCAAGTTGAAATTGCAATCAGTACAAGTGGT
GGAAGTATTTATTTATGGGACATAAAGACAGACAATAATGAGCAACTTTTGCCTGAAATG
AATGTTTCACTAAATAGCGTTGATATAAGTTCAAATGGAAAATATATGGCAGCAATAAAT
AATAAAGGAAGTTGCTACATTTGGGATTTAAAATCAGAAGGAAAACAATTGACAAAAACA
AGTGCAAAAATTAAATTTGTCGCTCATCAACGTTATGGTTTGAAATGTAAATTTTCACCT
GATTCACAACTTTTAGTCACAACAGGCGGGGATGGTACTGCACTAAATATATTTTCATTT
CAAGCAGTGATGGATCAGCGAGATTGTGGAAAATTGAAACAAAAAGCATCGAAAGAGAAT
ATTTGGGACATTCAAAGGCTTTGACTGCAATTGCTTTTAGAGATGAATTTGTTAAAATTT
CTAATTAA

>g17274.t3 Gene=g17274 Length=267
MVQTEGDPILATGGYDHTIKIWAPYSGTSIKTLQHSDSQVNALVIKNYLAAGGFQSIRLY
DLNASTNPLINFEGVSKNVTSVGFQEDGRFMYTGSEDCRVRIWDLNCPQPVCKRMFDCLT
PVASVCLHPNQVEIAISTSGGSIYLWDIKTDNNEQLLPEMNVSLNSVDISSNGKYMAAIN
NKGSCYIWDLKSEGKQLTKTSAKIKFVAHQRYGLKCKFSPDSQLLVTTGGDGTALNIFSF
QAVMDQRDCGKLKQKASKENIWDIQRL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g17274.t3 Gene3D G3DSA:2.130.10.10 - 7 265 2.4E-72
4 g17274.t3 PANTHER PTHR19842:SF0 TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8 6 263 2.2E-75
5 g17274.t3 PANTHER PTHR19842 G BETA-LIKE PROTEIN GBL 6 263 2.2E-75
2 g17274.t3 Pfam PF00400 WD domain, G-beta repeat 9 22 0.15
3 g17274.t3 Pfam PF00400 WD domain, G-beta repeat 72 104 3.7E-5
1 g17274.t3 Pfam PF07569 TUP1-like enhancer of split 155 203 2.9E-4
12 g17274.t3 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 91 105 -
14 g17274.t3 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 1 233 24.916
15 g17274.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 1 32 8.904
16 g17274.t3 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 72 106 13.148
10 g17274.t3 SMART SM00320 WD40_4 26 61 30.0
9 g17274.t3 SMART SM00320 WD40_4 65 104 9.8E-7
8 g17274.t3 SMART SM00320 WD40_4 109 147 1.8
7 g17274.t3 SMART SM00320 WD40_4 150 189 1.3
11 g17274.t3 SMART SM00320 WD40_4 199 239 0.35
6 g17274.t3 SUPERFAMILY SSF50978 WD40 repeat-like 8 240 1.32E-46

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:0031931 TORC1 complex CC
GO:0031929 TOR signaling BP
GO:0031932 TORC2 complex CC
GO:0005515 protein binding MF
GO:0006355 regulation of transcription, DNA-templated BP

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.

Raw TPM values