Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Toll-like receptor 7.

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_1 g10635 g10635.t1 isoform g10635.t1 10972535 10974203
chr_1 g10635 g10635.t1 exon g10635.t1.exon1 10972535 10972658
chr_1 g10635 g10635.t1 cds g10635.t1.CDS1 10972535 10972658
chr_1 g10635 g10635.t1 exon g10635.t1.exon2 10973761 10974203
chr_1 g10635 g10635.t1 cds g10635.t1.CDS2 10973761 10974203
chr_1 g10635 g10635.t1 TSS g10635.t1 NA NA
chr_1 g10635 g10635.t1 TTS g10635.t1 NA NA

Sequences

>g10635.t1 Gene=g10635 Length=567
ATGATTGCACAAAATGCATTTATTGATTTAAGAAATTTACATCAATTACTTTTGTCAAAT
AATCAATTAAAAGTGATCGAATCGAAGCATTTTGCTGGACTTTATTCATTAAATCAGCTC
ATCTTAGAATCAAATGAAATTTCAAATATTCATCCAACTGCATTTGATCATCTCATCAAT
TCTGTCGTTGATTTAAGTTTAAATGATAACAAATTAAAAAGAATTCCTGATTCAATAAAG
AAATTGAGAAATTTACAAGCTTTAGATTTGGGTAAAAATCAAATAAGTGAAATTGAAAGT
GACTCATTTGATGGATTAGAACAACTTGCTGGCTTAAGATTGACTGATAATCAAATTACA
GCCATCACAAAAGGTGCATTTGTTGCACTCAAATCAATTCATGTGCTCAATTTTGCATCA
AATAAAATCAGACATGTCGATCATGCTGGTTGGAGTTTAAATAAAGTTATTAATTTTAAT
CATTCAATTAATGACCATGAAGAGCATTTGATTGCCGAGAAGAGAATTTTTTGGATGATT
TTGAACTTGATTGAATCAATTGGATAA

>g10635.t1 Gene=g10635 Length=188
MIAQNAFIDLRNLHQLLLSNNQLKVIESKHFAGLYSLNQLILESNEISNIHPTAFDHLIN
SVVDLSLNDNKLKRIPDSIKKLRNLQALDLGKNQISEIESDSFDGLEQLAGLRLTDNQIT
AITKGAFVALKSIHVLNFASNKIRHVDHAGWSLNKVINFNHSINDHEEHLIAEKRIFWMI
LNLIESIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10635.t1 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 1 58 0.0000
11 g10635.t1 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 59 174 0.0000
2 g10635.t1 PANTHER PTHR45836:SF8 TOLL-LIKE RECEPTOR 6 2 157 0.0000
3 g10635.t1 PANTHER PTHR45836 SLIT HOMOLOG 2 157 0.0000
1 g10635.t1 Pfam PF13855 Leucine rich repeat 64 119 0.0000
13 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 12 33 7.0730
18 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 36 57 6.1180
15 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 61 82 6.0720
14 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 84 105 7.9660
17 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 108 129 5.3630
16 g10635.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 132 153 4.7780
6 g10635.t1 SMART SM00369 LRR_typ_2 10 33 0.9000
7 g10635.t1 SMART SM00369 LRR_typ_2 34 57 0.0600
9 g10635.t1 SMART SM00369 LRR_typ_2 59 81 360.0000
5 g10635.t1 SMART SM00369 LRR_typ_2 82 105 0.0025
10 g10635.t1 SMART SM00369 LRR_typ_2 106 129 6.0000
8 g10635.t1 SMART SM00369 LRR_typ_2 130 153 72.0000
4 g10635.t1 SUPERFAMILY SSF52058 L domain-like 10 167 0.0000

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.

Raw TPM values