Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t2 isoform g13343.t2 29382964 29384163
chr_1 g13343 g13343.t2 exon g13343.t2.exon1 29382964 29383381
chr_1 g13343 g13343.t2 cds g13343.t2.CDS1 29382964 29383381
chr_1 g13343 g13343.t2 exon g13343.t2.exon2 29383441 29383508
chr_1 g13343 g13343.t2 cds g13343.t2.CDS2 29383441 29383508
chr_1 g13343 g13343.t2 exon g13343.t2.exon3 29383568 29383691
chr_1 g13343 g13343.t2 cds g13343.t2.CDS3 29383568 29383691
chr_1 g13343 g13343.t2 exon g13343.t2.exon4 29383955 29384163
chr_1 g13343 g13343.t2 cds g13343.t2.CDS4 29383955 29384163
chr_1 g13343 g13343.t2 TSS g13343.t2 NA NA
chr_1 g13343 g13343.t2 TTS g13343.t2 NA NA

Sequences

>g13343.t2 Gene=g13343 Length=819
ATGAGAACGATTATATTTTCGATAATTATTTTATTGAGATCGAATTTCACACAAGCAAGG
CATGACCAATTTTATTTTTCACACCATCAACATCATCATCCGCACTATTATCAAACAAAT
GAGCCGAATGATTTATCGCTTTGGATAAGTGAACAGCAGGTGAAAATGTTTAGTGGCTAC
TCTATGCGAATTTACGCAATCGATAATGGAAGAGTTAATCCACTTTTAAGAGATCCCGCT
TTTGACACACTTATGCCAATTATTCCACCAGAAATTATGTCTATGAATTTTACATGGACT
GCTGGAAAAAGAAAATATCGCTATCATTTTGACCATATGATGTCACTTGATGAAAAAGTA
TTGCTAGCACCAGTAATTTCAATAAGACCAAAAGGAAGAATCCCACCTGAACCAAAACAA
TTCAGTGTCATGCTTCCATGCTCAAATCTCACATCAGGAATAGCAAAATTTACACTTGGT
CTTCAAATAACTCGCGCAAAAGGAAAATTTCTACCTGGCACACCATTACGTTTTACATTG
CGCAAAGAATGCAATTTGAATAGAGGTATGAAATCTTCTACTCTTGATTCTACTCCGGCT
TTGTTGCAAGGTGGACCAGATCCCGAATGTGATAAAAAATGTCTCAATGGTGGTTCATGT
ACAAAAAATAAAATCTGTAAATGTGCTGAAGGCTATATTGGACAAAATTGTGAACAAGCA
TTGTGTTTTCCACAATGTATGAATGGTGGTAATTGTTCAGCACCTGCTATTTGCTCATGT
CCAAAAGGCTATCAAGGGAGATATTGTGAAGGAGGTTAG

>g13343.t2 Gene=g13343 Length=272
MRTIIFSIIILLRSNFTQARHDQFYFSHHQHHHPHYYQTNEPNDLSLWISEQQVKMFSGY
SMRIYAIDNGRVNPLLRDPAFDTLMPIIPPEIMSMNFTWTAGKRKYRYHFDHMMSLDEKV
LLAPVISIRPKGRIPPEPKQFSVMLPCSNLTSGIAKFTLGLQITRAKGKFLPGTPLRFTL
RKECNLNRGMKSSTLDSTPALLQGGPDPECDKKCLNGGSCTKNKICKCAEGYIGQNCEQA
LCFPQCMNGGNCSAPAICSCPKGYQGRYCEGG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13343.t2 CDD cd00054 EGF_CA 209 238 0.00278343
8 g13343.t2 Gene3D G3DSA:2.60.40.2170 - 41 187 1.3E-51
6 g13343.t2 Gene3D G3DSA:2.10.25.10 Laminin 210 240 1.9E-8
7 g13343.t2 Gene3D G3DSA:2.10.25.10 Laminin 242 271 2.3E-6
2 g13343.t2 PANTHER PTHR14949:SF32 WNT INHIBITORY FACTOR 1 39 271 6.7E-65
3 g13343.t2 PANTHER PTHR14949 EGF-LIKE-DOMAIN, MULTIPLE 7, 8 39 271 6.7E-65
1 g13343.t2 Pfam PF02019 WIF domain 47 184 6.3E-34
10 g13343.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
11 g13343.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
12 g13343.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
13 g13343.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
9 g13343.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 272 -
16 g13343.t2 ProSitePatterns PS01186 EGF-like domain signature 2. 226 237 -
18 g13343.t2 ProSitePatterns PS00022 EGF-like domain signature 1. 226 237 -
15 g13343.t2 ProSitePatterns PS01186 EGF-like domain signature 2. 258 269 -
17 g13343.t2 ProSitePatterns PS00022 EGF-like domain signature 1. 258 269 -
22 g13343.t2 ProSiteProfiles PS50814 WIF domain profile. 47 184 35.32
23 g13343.t2 ProSiteProfiles PS50026 EGF-like domain profile. 206 238 14.426
24 g13343.t2 ProSiteProfiles PS50026 EGF-like domain profile. 239 270 10.544
19 g13343.t2 SMART SM00469 WIF_1 44 186 6.2E-13
21 g13343.t2 SMART SM00181 egf_5 209 238 3.3E-4
20 g13343.t2 SMART SM00181 egf_5 241 270 0.021
4 g13343.t2 SUPERFAMILY SSF57196 EGF/Laminin 209 242 7.39E-5
5 g13343.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -

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