Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Stress-induced-phosphoprotein 1.

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_2 g5018 g5018.t7 isoform g5018.t7 6476492 6477613
chr_2 g5018 g5018.t7 exon g5018.t7.exon1 6476492 6477170
chr_2 g5018 g5018.t7 cds g5018.t7.CDS1 6476494 6477078
chr_2 g5018 g5018.t7 TTS g5018.t7 6476968 6476968
chr_2 g5018 g5018.t7 exon g5018.t7.exon2 6477244 6477613
chr_2 g5018 g5018.t7 TSS g5018.t7 6477752 6477752

Sequences

>g5018.t7 Gene=g5018 Length=1049
ATGGCAGATGTAAGTATTATTTAATAAATAAACTATTAATGTTTATCTAAAGAAAGTATT
ACATTGCAAAAAAAATTTATTCAACAGATAAATCAGCTCAAAGAAAAAGGAAATGCTGCT
TTGACAGCAGGCAGGAATGAAGAAGCTATTGAAGCTTATAGCGAGGCAATTAAATTAGAT
GACTCAAATCATGTTCTTTACTCAAATCGTTCTGCTGCATATTTAAAAGCCGGAAAACTT
GAGGAATCGCTTAAAGATGCTGAAAAGACTATTGAGCTCAATTCAAGTTGGCCCAAAGGA
TATTCACGAAAAGGAGCTGCTCTCTTTGCACTCGAGCGATATGAAGAAGCTTTTACAGCA
TACAACAAAGGTCTCGAATTTGATGCAAATAATCAAGCACTTCTTCAAGGACAGCAGCAA
GTAAAAGAAGCATTGATTAATCAACTTTTAAAAAATCAACCGATGGACGTTGACCCTCCA
GAACAAAGTAAACCAGCAAAACAACCATCACCACCTCCAGCGAAAAAACCAGCACCAGAA
GATGAGAATTTACCCGAAAATAAAAAGCTCGCCAAAAAAGAGAAGGATGAAGGAAATGCA
GCATACAAAAAGAAAGATTTTGCAACTGCTCTCACTCATTATAACAAAGCTATCGAACAT
GATCCTACTGACATAACATTCTATAGTAATATTGCTGCTGTATATTTTGAACAGAAAGAC
TTCCGCAAGTGCATCAGTGAGTGTGAAAAGGGAATTGAAGTAGGTCGTGAGAACCGTGCT
GATTATAAATTAATTGCAAAAGCTTTAGCAAGAATAGCTAACAGTTATAAGAAATTGGGA
GAATATAAAAATGCTAAGACGTACTATGAAAAATCTCTATCAGAACATCGAACTCCCGAA
GTGAAAACTATGCTATCAGAAGTAGAAAAAATTATTAATGAAGAGGAACGTCGTGCTTTC
ATAGATCCTGCAAAGGCTGAAGAAGAGAAAGAAAAAGGAAATGAATATTTCAAAAAGGGC
GATTTTTCAACTGCAATAAAGCATTATAC

>g5018.t7 Gene=g5018 Length=195
MDVDPPEQSKPAKQPSPPPAKKPAPEDENLPENKKLAKKEKDEGNAAYKKKDFATALTHY
NKAIEHDPTDITFYSNIAAVYFEQKDFRKCISECEKGIEVGRENRADYKLIAKALARIAN
SYKKLGEYKNAKTYYEKSLSEHRTPEVKTMLSEVEKIINEEERRAFIDPAKAEEEKEKGN
EYFKKGDFSTAIKHY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g5018.t7 Gene3D G3DSA:1.25.40.10 - 34 162 1.1E-43
14 g5018.t7 Gene3D G3DSA:1.25.40.10 - 163 195 2.6E-7
12 g5018.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 45 -
10 g5018.t7 MobiDBLite mobidb-lite consensus disorder prediction 10 24 -
11 g5018.t7 MobiDBLite mobidb-lite consensus disorder prediction 25 45 -
3 g5018.t7 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 12 195 3.6E-63
4 g5018.t7 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 12 195 3.6E-63
1 g5018.t7 Pfam PF13414 TPR repeat 44 84 4.3E-10
2 g5018.t7 Pfam PF13181 Tetratricopeptide repeat 112 140 9.4E-6
16 g5018.t7 ProSiteProfiles PS50005 TPR repeat profile. 37 70 9.086
19 g5018.t7 ProSiteProfiles PS50293 TPR repeat region circular profile. 37 145 18.154
15 g5018.t7 ProSiteProfiles PS50005 TPR repeat profile. 71 104 6.579
17 g5018.t7 ProSiteProfiles PS50005 TPR repeat profile. 112 145 8.555
18 g5018.t7 ProSiteProfiles PS50293 TPR repeat region circular profile. 172 195 7.206
8 g5018.t7 SMART SM00028 tpr_5 37 70 0.0021
7 g5018.t7 SMART SM00028 tpr_5 71 104 0.15
9 g5018.t7 SMART SM00028 tpr_5 112 145 6.3E-5
6 g5018.t7 SUPERFAMILY SSF48452 TPR-like 35 160 5.69E-48
5 g5018.t7 SUPERFAMILY SSF48452 TPR-like 169 195 1.17E-6

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5018/g5018.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5018.t7.fa.iupred3.txt does not exist

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