Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein shifted.

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 g13343 g13343.t3 isoform g13343.t3 29383958 29385333
chr_1 g13343 g13343.t3 exon g13343.t3.exon1 29383958 29384158
chr_1 g13343 g13343.t3 cds g13343.t3.CDS1 29384083 29384158
chr_1 g13343 g13343.t3 exon g13343.t3.exon2 29384835 29384930
chr_1 g13343 g13343.t3 cds g13343.t3.CDS2 29384835 29384930
chr_1 g13343 g13343.t3 exon g13343.t3.exon3 29384989 29385333
chr_1 g13343 g13343.t3 cds g13343.t3.CDS3 29384989 29385257
chr_1 g13343 g13343.t3 TTS g13343.t3 29385326 29385326
chr_1 g13343 g13343.t3 TSS g13343.t3 NA NA

Sequences

>g13343.t3 Gene=g13343 Length=642
GACCAGATCCCGAATGTGATAAAAAATGTCTCAATGGTGGTTCATGTACAAAAAATAAAA
TCTGTAAATGTGCTGAAGGCTATATTGGACAAAATTGTGAACAAGCATTGTGTTTTCCAC
AATGTATGAATGGTGGTAATTGTTCAGCACCTGCTATTTGCTCATGTCCAAAAGGCTATC
AAGGGAGATATTGTGAAGGAGGAATTTGCACAGAAAAATGTTTGAATGGAGGTAAATGTG
TACAGAAAGACACTTGTCAATGTCCCAAAGGATATTATGGCTTGAGATGTCAATTGTCTA
AATGTGTTGTGCCATGTTTGAATGGAGGAAAGTGCAGAGGAAATAATGTATGCCGTTGCA
CAGACGGTTGGGCTGGAAATCATTGTGAAATAGGGAGAAAGATCCAAAGATCGATTTGTA
AAAAACCTTGCAAAAATGGATTCTGTCTTTCCACTGGTGTATGTCAATGTAAAAAGGGAT
GGGTAGGAAAATTCTGTAATCAAAGAAATAAGCGCAGAAGAAACACAACAAAGCTGGCAA
ATGTGAATTCAAAGAAGCAAAATTGACTTTCATTAAAAACTTAAAATTATTTTTGTGATA
TCTTTTAAATATGACAATAAAATTTTTCAAACACTAATAAAA

>g13343.t3 Gene=g13343 Length=146
MNGGNCSAPAICSCPKGYQGRYCEGGICTEKCLNGGKCVQKDTCQCPKGYYGLRCQLSKC
VVPCLNGGKCRGNNVCRCTDGWAGNHCEIGRKIQRSICKKPCKNGFCLSTGVCQCKKGWV
GKFCNQRNKRRRNTTKLANVNSKKQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g13343.t3 Gene3D G3DSA:2.10.25.10 Laminin 1 26 1.7E-6
16 g13343.t3 Gene3D G3DSA:2.10.25.10 Laminin 28 59 2.1E-9
19 g13343.t3 Gene3D G3DSA:2.10.25.10 Laminin 60 91 8.9E-9
18 g13343.t3 Gene3D G3DSA:2.10.25.10 Laminin 92 128 2.1E-8
2 g13343.t3 PANTHER PTHR14949:SF32 WNT INHIBITORY FACTOR 1 1 141 1.1E-37
3 g13343.t3 PANTHER PTHR14949 EGF-LIKE-DOMAIN, MULTIPLE 7, 8 1 141 1.1E-37
1 g13343.t3 Pfam PF00008 EGF-like domain 28 54 3.2E-5
10 g13343.t3 ProSitePatterns PS01186 EGF-like domain signature 2. 44 55 -
13 g13343.t3 ProSitePatterns PS00022 EGF-like domain signature 1. 44 55 -
12 g13343.t3 ProSitePatterns PS01186 EGF-like domain signature 2. 76 87 -
15 g13343.t3 ProSitePatterns PS00022 EGF-like domain signature 1. 76 87 -
11 g13343.t3 ProSitePatterns PS01186 EGF-like domain signature 2. 113 124 -
14 g13343.t3 ProSitePatterns PS00022 EGF-like domain signature 1. 113 124 -
22 g13343.t3 ProSiteProfiles PS50026 EGF-like domain profile. 24 56 15.48
20 g13343.t3 ProSiteProfiles PS50026 EGF-like domain profile. 57 88 11.199
21 g13343.t3 ProSiteProfiles PS50026 EGF-like domain profile. 94 125 8.502
8 g13343.t3 SMART SM00181 egf_5 1 24 56.0
7 g13343.t3 SMART SM00181 egf_5 27 56 0.0027
9 g13343.t3 SMART SM00181 egf_5 59 88 0.0048
6 g13343.t3 SMART SM00181 egf_5 97 125 0.014
4 g13343.t3 SUPERFAMILY SSF57196 EGF/Laminin 28 59 1.9E-5
5 g13343.t3 SUPERFAMILY SSF57196 EGF/Laminin 59 90 1.97E-5

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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