Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t5 TTS g5018.t5 6475539 6475539
chr_2 g5018 g5018.t5 isoform g5018.t5 6476145 6477140
chr_2 g5018 g5018.t5 exon g5018.t5.exon1 6476145 6477140
chr_2 g5018 g5018.t5 cds g5018.t5.CDS1 6476146 6477078
chr_2 g5018 g5018.t5 TSS g5018.t5 6477752 6477752

Sequences

>g5018.t5 Gene=g5018 Length=996
TTCTTCAAGGACAGCAGCAAGTAAAAGAAGCATTGATTAATCAACTTTTAAAAAATCAAC
CGATGGACGTTGACCCTCCAGAACAAAGTAAACCAGCAAAACAACCATCACCACCTCCAG
CGAAAAAACCAGCACCAGAAGATGAGAATTTACCCGAAAATAAAAAGCTCGCCAAAAAAG
AGAAGGATGAAGGAAATGCAGCATACAAAAAGAAAGATTTTGCAACTGCTCTCACTCATT
ATAACAAAGCTATCGAACATGATCCTACTGACATAACATTCTATAGTAATATTGCTGCTG
TATATTTTGAACAGAAAGACTTCCGCAAGTGCATCAGTGAGTGTGAAAAGGGAATTGAAG
TAGGTCGTGAGAACCGTGCTGATTATAAATTAATTGCAAAAGCTTTAGCAAGAATAGCTA
ACAGTTATAAGAAATTGGGAGAATATAAAAATGCTAAGACGTACTATGAAAAATCTCTAT
CAGAACATCGAACTCCCGAAGTGAAAACTATGCTATCAGAAGTAGAAAAAATTATTAATG
AAGAGGAACGTCGTGCTTTCATAGATCCTGCAAAGGCTGAAGAAGAGAAAGAAAAAGGAA
ATGAATATTTCAAAAAGGGCGATTTTTCAACTGCAATAAAGCATTATACAGAAGCGATAA
ATCGCAATCCAGATGATCCAAAACTGTATTCCAATCGTGCTGCCTGTTATACTAAACTTG
CTGCATTTGATTTAGGTTTGAAAGATTGTGAAATGTGTACGAAATTAGATGAAAAGTTTA
TCAAAGGTTGGATCAGAAAGGGAAAAATTTTACAAGGAATGCAACAACCATCGAAAGCAC
TTGCTGCATATCAAAAGGCTCTCGACATTGACCCCACAAACGGTGAAGCTCTTGAAGGTT
ACCGTGCTTGCACAATGGCAGTTCATTCCAATCCTGAAGAAGTGAGAAAAAAGGCAATGA
ATGATCCTGAAATTCAATCAATTCTCAAAGATCCAG

>g5018.t5 Gene=g5018 Length=311
MDVDPPEQSKPAKQPSPPPAKKPAPEDENLPENKKLAKKEKDEGNAAYKKKDFATALTHY
NKAIEHDPTDITFYSNIAAVYFEQKDFRKCISECEKGIEVGRENRADYKLIAKALARIAN
SYKKLGEYKNAKTYYEKSLSEHRTPEVKTMLSEVEKIINEEERRAFIDPAKAEEEKEKGN
EYFKKGDFSTAIKHYTEAINRNPDDPKLYSNRAACYTKLAAFDLGLKDCEMCTKLDEKFI
KGWIRKGKILQGMQQPSKALAAYQKALDIDPTNGEALEGYRACTMAVHSNPEEVRKKAMN
DPEIQSILKDP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5018.t5 Gene3D G3DSA:1.25.40.10 - 34 160 3.7E-43
18 g5018.t5 Gene3D G3DSA:1.25.40.10 - 161 289 4.1E-44
16 g5018.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 44 -
15 g5018.t5 MobiDBLite mobidb-lite consensus disorder prediction 10 24 -
17 g5018.t5 MobiDBLite mobidb-lite consensus disorder prediction 25 44 -
5 g5018.t5 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 12 311 9.8E-111
6 g5018.t5 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 12 311 9.8E-111
3 g5018.t5 Pfam PF13414 TPR repeat 44 84 8.9E-10
4 g5018.t5 Pfam PF13181 Tetratricopeptide repeat 112 140 1.8E-5
2 g5018.t5 Pfam PF13414 TPR repeat 179 218 6.6E-10
1 g5018.t5 Pfam PF00515 Tetratricopeptide repeat 241 273 1.1E-7
21 g5018.t5 ProSiteProfiles PS50005 TPR repeat profile. 37 70 9.086
25 g5018.t5 ProSiteProfiles PS50293 TPR repeat region circular profile. 37 273 27.821
20 g5018.t5 ProSiteProfiles PS50005 TPR repeat profile. 71 104 6.579
22 g5018.t5 ProSiteProfiles PS50005 TPR repeat profile. 112 145 8.555
23 g5018.t5 ProSiteProfiles PS50005 TPR repeat profile. 172 205 11.24
24 g5018.t5 ProSiteProfiles PS50005 TPR repeat profile. 240 273 10.119
10 g5018.t5 SMART SM00028 tpr_5 37 70 0.0021
9 g5018.t5 SMART SM00028 tpr_5 71 104 0.15
11 g5018.t5 SMART SM00028 tpr_5 112 145 6.3E-5
12 g5018.t5 SMART SM00028 tpr_5 172 205 3.7E-5
13 g5018.t5 SMART SM00028 tpr_5 206 239 0.081
14 g5018.t5 SMART SM00028 tpr_5 240 273 6.9E-6
8 g5018.t5 SUPERFAMILY SSF48452 TPR-like 35 160 1.16E-47
7 g5018.t5 SUPERFAMILY SSF48452 TPR-like 171 284 1.9E-39

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5018/g5018.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5018.t5.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