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.t3 isoform g5018.t3 6475521 6477613
chr_2 g5018 g5018.t3 exon g5018.t3.exon1 6475521 6476035
chr_2 g5018 g5018.t3 TTS g5018.t3 6475539 6475539
chr_2 g5018 g5018.t3 cds g5018.t3.CDS1 6475963 6476035
chr_2 g5018 g5018.t3 exon g5018.t3.exon2 6476093 6477170
chr_2 g5018 g5018.t3 cds g5018.t3.CDS2 6476093 6477078
chr_2 g5018 g5018.t3 exon g5018.t3.exon3 6477244 6477613
chr_2 g5018 g5018.t3 TSS g5018.t3 6477752 6477752

Sequences

>g5018.t3 Gene=g5018 Length=1963
ATGGCAGATGTAAGTATTATTTAATAAATAAACTATTAATGTTTATCTAAAGAAAGTATT
ACATTGCAAAAAAAATTTATTCAACAGATAAATCAGCTCAAAGAAAAAGGAAATGCTGCT
TTGACAGCAGGCAGGAATGAAGAAGCTATTGAAGCTTATAGCGAGGCAATTAAATTAGAT
GACTCAAATCATGTTCTTTACTCAAATCGTTCTGCTGCATATTTAAAAGCCGGAAAACTT
GAGGAATCGCTTAAAGATGCTGAAAAGACTATTGAGCTCAATTCAAGTTGGCCCAAAGGA
TATTCACGAAAAGGAGCTGCTCTCTTTGCACTCGAGCGATATGAAGAAGCTTTTACAGCA
TACAACAAAGGTCTCGAATTTGATGCAAATAATCAAGCACTTCTTCAAGGACAGCAGCAA
GTAAAAGAAGCATTGATTAATCAACTTTTAAAAAATCAACCGATGGACGTTGACCCTCCA
GAACAAAGTAAACCAGCAAAACAACCATCACCACCTCCAGCGAAAAAACCAGCACCAGAA
GATGAGAATTTACCCGAAAATAAAAAGCTCGCCAAAAAAGAGAAGGATGAAGGAAATGCA
GCATACAAAAAGAAAGATTTTGCAACTGCTCTCACTCATTATAACAAAGCTATCGAACAT
GATCCTACTGACATAACATTCTATAGTAATATTGCTGCTGTATATTTTGAACAGAAAGAC
TTCCGCAAGTGCATCAGTGAGTGTGAAAAGGGAATTGAAGTAGGTCGTGAGAACCGTGCT
GATTATAAATTAATTGCAAAAGCTTTAGCAAGAATAGCTAACAGTTATAAGAAATTGGGA
GAATATAAAAATGCTAAGACGTACTATGAAAAATCTCTATCAGAACATCGAACTCCCGAA
GTGAAAACTATGCTATCAGAAGTAGAAAAAATTATTAATGAAGAGGAACGTCGTGCTTTC
ATAGATCCTGCAAAGGCTGAAGAAGAGAAAGAAAAAGGAAATGAATATTTCAAAAAGGGC
GATTTTTCAACTGCAATAAAGCATTATACAGAAGCGATAAATCGCAATCCAGATGATCCA
AAACTGTATTCCAATCGTGCTGCCTGTTATACTAAACTTGCTGCATTTGATTTAGGTTTG
AAAGATTGTGAAATGTGTACGAAATTAGATGAAAAGTTTATCAAAGGTTGGATCAGAAAG
GGAAAAATTTTACAAGGAATGCAACAACCATCGAAAGCACTTGCTGCATATCAAAAGGCT
CTCGACATTGACCCCACAAACGGTGAAGCTCTTGAAGGTTACCGTGCTTGCACAATGGCA
GTTCATTCCAATCCTGAAGAAGTGAGAAAAAAGGCAATGAATGATCCTGAAATTCAATCA
ATTCTCAAAGATCCAGCTATGAGACTTATTCTCGAGCAAATGCAGTCTGATCCCAAAGCT
GTTCAAGAGCATTTGAGAAATCCAGAAGTTGCAAACAAAATTCAAAAATTATTAGAATCT
GGTATCATTCAAATACACTAAATTTAAGGAATATCATTTACAAAACAAATAGGATTTATG
GCGCTTAATCAAAGAAAGAGAGAGAGAGAGATGAGCAACAAAATTGTCTTGATAAGATTT
TTGTAATTTTGCTATATTAACAAACACCACACACACTCATTCTTTGTCTCATTTAAAAAC
ACGTACACTTACATACTTATCTATTCTTCTTTATAAGAAAGCTATTAAAGATTTCTTTGA
TTAATAATTACAAAACATAAAATTGCCATGAAATTACTACATTCTTATTCTTATAAATTT
TTCTTTTTGGCGGATAAAATGGTATGATACTGTTTGAATTCTTGTTGGCTTAATTTTTCT
ATTAATGTTTGCGTTAATTGAACATGGTTCTCTATTTCAGCATACAAAAAAAAGGAAAAA
TAAAAAAATTTAAGTAGAAAAATGCAAATAATTTTTTTTTTCT

>g5018.t3 Gene=g5018 Length=352
MDVDPPEQSKPAKQPSPPPAKKPAPEDENLPENKKLAKKEKDEGNAAYKKKDFATALTHY
NKAIEHDPTDITFYSNIAAVYFEQKDFRKCISECEKGIEVGRENRADYKLIAKALARIAN
SYKKLGEYKNAKTYYEKSLSEHRTPEVKTMLSEVEKIINEEERRAFIDPAKAEEEKEKGN
EYFKKGDFSTAIKHYTEAINRNPDDPKLYSNRAACYTKLAAFDLGLKDCEMCTKLDEKFI
KGWIRKGKILQGMQQPSKALAAYQKALDIDPTNGEALEGYRACTMAVHSNPEEVRKKAMN
DPEIQSILKDPAMRLILEQMQSDPKAVQEHLRNPEVANKIQKLLESGIIQIH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g5018.t3 Gene3D G3DSA:1.25.40.10 - 34 160 4.9E-43
20 g5018.t3 Gene3D G3DSA:1.25.40.10 - 161 287 5.4E-44
22 g5018.t3 Gene3D G3DSA:1.10.260.100 - 288 351 9.9E-25
18 g5018.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 44 -
17 g5018.t3 MobiDBLite mobidb-lite consensus disorder prediction 10 24 -
19 g5018.t3 MobiDBLite mobidb-lite consensus disorder prediction 25 44 -
6 g5018.t3 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 12 351 3.8E-132
7 g5018.t3 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 12 351 3.8E-132
3 g5018.t3 Pfam PF13414 TPR repeat 44 84 1.1E-9
5 g5018.t3 Pfam PF13181 Tetratricopeptide repeat 112 140 2.2E-5
2 g5018.t3 Pfam PF13414 TPR repeat 179 218 7.9E-10
1 g5018.t3 Pfam PF00515 Tetratricopeptide repeat 241 273 1.3E-7
4 g5018.t3 Pfam PF17830 STI1 domain 292 344 1.8E-16
24 g5018.t3 ProSiteProfiles PS50005 TPR repeat profile. 37 70 9.086
28 g5018.t3 ProSiteProfiles PS50293 TPR repeat region circular profile. 37 273 27.821
23 g5018.t3 ProSiteProfiles PS50005 TPR repeat profile. 71 104 6.579
25 g5018.t3 ProSiteProfiles PS50005 TPR repeat profile. 112 145 8.555
26 g5018.t3 ProSiteProfiles PS50005 TPR repeat profile. 172 205 11.24
27 g5018.t3 ProSiteProfiles PS50005 TPR repeat profile. 240 273 10.119
11 g5018.t3 SMART SM00028 tpr_5 37 70 0.0021
10 g5018.t3 SMART SM00028 tpr_5 71 104 0.15
12 g5018.t3 SMART SM00028 tpr_5 112 145 6.3E-5
13 g5018.t3 SMART SM00028 tpr_5 172 205 3.7E-5
14 g5018.t3 SMART SM00028 tpr_5 206 239 0.081
15 g5018.t3 SMART SM00028 tpr_5 240 273 6.9E-6
16 g5018.t3 SMART SM00727 CBM 301 340 5.4E-10
9 g5018.t3 SUPERFAMILY SSF48452 TPR-like 35 160 1.43E-47
8 g5018.t3 SUPERFAMILY SSF48452 TPR-like 171 284 2.47E-39

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5018/g5018.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5018.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

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