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.t4 TTS g5018.t4 6475539 6475539
chr_2 g5018 g5018.t4 isoform g5018.t4 6475963 6477613
chr_2 g5018 g5018.t4 exon g5018.t4.exon1 6475963 6477170
chr_2 g5018 g5018.t4 cds g5018.t4.CDS1 6476089 6477170
chr_2 g5018 g5018.t4 exon g5018.t4.exon2 6477244 6477526
chr_2 g5018 g5018.t4 cds g5018.t4.CDS2 6477244 6477526
chr_2 g5018 g5018.t4 exon g5018.t4.exon3 6477605 6477613
chr_2 g5018 g5018.t4 cds g5018.t4.CDS3 6477605 6477613
chr_2 g5018 g5018.t4 TSS g5018.t4 6477752 6477752

Sequences

>g5018.t4 Gene=g5018 Length=1500
ATGGCAGATATAAATCAGCTCAAAGAAAAAGGAAATGCTGCTTTGACAGCAGGCAGGAAT
GAAGAAGCTATTGAAGCTTATAGCGAGGCAATTAAATTAGATGACTCAAATCATGTTCTT
TACTCAAATCGTTCTGCTGCATATTTAAAAGCCGGAAAACTTGAGGAATCGCTTAAAGAT
GCTGAAAAGACTATTGAGCTCAATTCAAGTTGGCCCAAAGGATATTCACGAAAAGGAGCT
GCTCTCTTTGCACTCGAGCGATATGAAGAAGCTTTTACAGCATACAACAAAGGTCTCGAA
TTTGATGCAAATAATCAAGCACTTCTTCAAGGACAGCAGCAAGTAAAAGAAGCATTGATT
AATCAACTTTTAAAAAATCAACCGATGGACGTTGACCCTCCAGAACAAAGTAAACCAGCA
AAACAACCATCACCACCTCCAGCGAAAAAACCAGCACCAGAAGATGAGAATTTACCCGAA
AATAAAAAGCTCGCCAAAAAAGAGAAGGATGAAGGAAATGCAGCATACAAAAAGAAAGAT
TTTGCAACTGCTCTCACTCATTATAACAAAGCTATCGAACATGATCCTACTGACATAACA
TTCTATAGTAATATTGCTGCTGTATATTTTGAACAGAAAGACTTCCGCAAGTGCATCAGT
GAGTGTGAAAAGGGAATTGAAGTAGGTCGTGAGAACCGTGCTGATTATAAATTAATTGCA
AAAGCTTTAGCAAGAATAGCTAACAGTTATAAGAAATTGGGAGAATATAAAAATGCTAAG
ACGTACTATGAAAAATCTCTATCAGAACATCGAACTCCCGAAGTGAAAACTATGCTATCA
GAAGTAGAAAAAATTATTAATGAAGAGGAACGTCGTGCTTTCATAGATCCTGCAAAGGCT
GAAGAAGAGAAAGAAAAAGGAAATGAATATTTCAAAAAGGGCGATTTTTCAACTGCAATA
AAGCATTATACAGAAGCGATAAATCGCAATCCAGATGATCCAAAACTGTATTCCAATCGT
GCTGCCTGTTATACTAAACTTGCTGCATTTGATTTAGGTTTGAAAGATTGTGAAATGTGT
ACGAAATTAGATGAAAAGTTTATCAAAGGTTGGATCAGAAAGGGAAAAATTTTACAAGGA
ATGCAACAACCATCGAAAGCACTTGCTGCATATCAAAAGGCTCTCGACATTGACCCCACA
AACGGTGAAGCTCTTGAAGGTTACCGTGCTTGCACAATGGCAGTTCATTCCAATCCTGAA
GAAGTGAGAAAAAAGGCAATGAATGATCCTGAAATTCAATCAATTCTCAAAGATCCAGCT
ATGAGACTTATTCTCGAGCAAATGCAGTCTGATCCCAAAGCTGTTCAAGAGTAGGTTTAT
GAAATTCATTATTTTATAAAGAAACTAATTTTATTTCATTTTTTTAGGCATTTGAGAAAT
CCAGAAGTTGCAAACAAAATTCAAAAATTATTAGAATCTGGTATCATTCAAATACACTAA

>g5018.t4 Gene=g5018 Length=457
MADINQLKEKGNAALTAGRNEEAIEAYSEAIKLDDSNHVLYSNRSAAYLKAGKLEESLKD
AEKTIELNSSWPKGYSRKGAALFALERYEEAFTAYNKGLEFDANNQALLQGQQQVKEALI
NQLLKNQPMDVDPPEQSKPAKQPSPPPAKKPAPEDENLPENKKLAKKEKDEGNAAYKKKD
FATALTHYNKAIEHDPTDITFYSNIAAVYFEQKDFRKCISECEKGIEVGRENRADYKLIA
KALARIANSYKKLGEYKNAKTYYEKSLSEHRTPEVKTMLSEVEKIINEEERRAFIDPAKA
EEEKEKGNEYFKKGDFSTAIKHYTEAINRNPDDPKLYSNRAACYTKLAAFDLGLKDCEMC
TKLDEKFIKGWIRKGKILQGMQQPSKALAAYQKALDIDPTNGEALEGYRACTMAVHSNPE
EVRKKAMNDPEIQSILKDPAMRLILEQMQSDPKAVQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
28 g5018.t4 Gene3D G3DSA:1.25.40.10 - 1 117 3.3E-39
26 g5018.t4 Gene3D G3DSA:1.25.40.10 - 162 288 8.2E-43
27 g5018.t4 Gene3D G3DSA:1.25.40.10 - 289 415 9.0E-44
29 g5018.t4 Gene3D G3DSA:1.10.260.100 - 416 457 7.7E-13
25 g5018.t4 MobiDBLite mobidb-lite consensus disorder prediction 130 160 -
24 g5018.t4 MobiDBLite mobidb-lite consensus disorder prediction 138 152 -
9 g5018.t4 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 4 123 3.1E-154
11 g5018.t4 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 4 123 3.1E-154
8 g5018.t4 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 140 457 3.1E-154
10 g5018.t4 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 140 457 3.1E-154
4 g5018.t4 Pfam PF13414 TPR repeat 11 52 6.0E-7
6 g5018.t4 Pfam PF13181 Tetratricopeptide repeat 74 105 0.018
3 g5018.t4 Pfam PF13414 TPR repeat 172 212 1.5E-9
7 g5018.t4 Pfam PF13181 Tetratricopeptide repeat 240 268 3.0E-5
2 g5018.t4 Pfam PF13414 TPR repeat 307 346 1.1E-9
1 g5018.t4 Pfam PF00515 Tetratricopeptide repeat 369 401 1.9E-7
5 g5018.t4 Pfam PF17830 STI1 domain 420 456 1.7E-9
35 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 4 37 9.352
38 g5018.t4 ProSiteProfiles PS50293 TPR repeat region circular profile. 4 401 32.773
30 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 38 71 7.169
32 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 72 105 9.499
36 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 165 198 9.086
33 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 199 232 6.579
37 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 240 273 8.555
31 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 300 333 11.24
34 g5018.t4 ProSiteProfiles PS50005 TPR repeat profile. 368 401 10.119
21 g5018.t4 SMART SM00028 tpr_5 4 37 0.0016
16 g5018.t4 SMART SM00028 tpr_5 38 71 0.52
18 g5018.t4 SMART SM00028 tpr_5 72 105 6.0E-5
22 g5018.t4 SMART SM00028 tpr_5 165 198 0.0021
19 g5018.t4 SMART SM00028 tpr_5 199 232 0.15
23 g5018.t4 SMART SM00028 tpr_5 240 273 6.3E-5
17 g5018.t4 SMART SM00028 tpr_5 300 333 3.7E-5
15 g5018.t4 SMART SM00028 tpr_5 334 367 0.081
20 g5018.t4 SMART SM00028 tpr_5 368 401 6.9E-6
14 g5018.t4 SUPERFAMILY SSF48452 TPR-like 5 116 1.33E-38
13 g5018.t4 SUPERFAMILY SSF48452 TPR-like 163 288 2.46E-47
12 g5018.t4 SUPERFAMILY SSF48452 TPR-like 299 412 4.17E-39

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5018/g5018.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5018.t4.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