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.t2 isoform g5018.t2 6475521 6476492
chr_2 g5018 g5018.t2 exon g5018.t2.exon1 6475521 6476035
chr_2 g5018 g5018.t2 TTS g5018.t2 6475539 6475539
chr_2 g5018 g5018.t2 cds g5018.t2.CDS1 6475963 6476035
chr_2 g5018 g5018.t2 exon g5018.t2.exon2 6476093 6476492
chr_2 g5018 g5018.t2 cds g5018.t2.CDS2 6476093 6476388
chr_2 g5018 g5018.t2 TSS g5018.t2 NA NA

Sequences

>g5018.t2 Gene=g5018 Length=915
CAGAAGCGATAAATCGCAATCCAGATGATCCAAAACTGTATTCCAATCGTGCTGCCTGTT
ATACTAAACTTGCTGCATTTGATTTAGGTTTGAAAGATTGTGAAATGTGTACGAAATTAG
ATGAAAAGTTTATCAAAGGTTGGATCAGAAAGGGAAAAATTTTACAAGGAATGCAACAAC
CATCGAAAGCACTTGCTGCATATCAAAAGGCTCTCGACATTGACCCCACAAACGGTGAAG
CTCTTGAAGGTTACCGTGCTTGCACAATGGCAGTTCATTCCAATCCTGAAGAAGTGAGAA
AAAAGGCAATGAATGATCCTGAAATTCAATCAATTCTCAAAGATCCAGCTATGAGACTTA
TTCTCGAGCAAATGCAGTCTGATCCCAAAGCTGTTCAAGAGCATTTGAGAAATCCAGAAG
TTGCAAACAAAATTCAAAAATTATTAGAATCTGGTATCATTCAAATACACTAAATTTAAG
GAATATCATTTACAAAACAAATAGGATTTATGGCGCTTAATCAAAGAAAGAGAGAGAGAG
AGATGAGCAACAAAATTGTCTTGATAAGATTTTTGTAATTTTGCTATATTAACAAACACC
ACACACACTCATTCTTTGTCTCATTTAAAAACACGTACACTTACATACTTATCTATTCTT
CTTTATAAGAAAGCTATTAAAGATTTCTTTGATTAATAATTACAAAACATAAAATTGCCA
TGAAATTACTACATTCTTATTCTTATAAATTTTTCTTTTTGGCGGATAAAATGGTATGAT
ACTGTTTGAATTCTTGTTGGCTTAATTTTTCTATTAATGTTTGCGTTAATTGAACATGGT
TCTCTATTTCAGCATACAAAAAAAAGGAAAAATAAAAAAATTTAAGTAGAAAAATGCAAA
TAATTTTTTTTTTCT

>g5018.t2 Gene=g5018 Length=122
MCTKLDEKFIKGWIRKGKILQGMQQPSKALAAYQKALDIDPTNGEALEGYRACTMAVHSN
PEEVRKKAMNDPEIQSILKDPAMRLILEQMQSDPKAVQEHLRNPEVANKIQKLLESGIIQ
IH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5018.t2 Gene3D G3DSA:1.25.40.10 - 1 57 0.0000000
9 g5018.t2 Gene3D G3DSA:1.10.260.100 - 58 121 0.0000000
3 g5018.t2 PANTHER PTHR22904:SF517 STRESS-INDUCED-PHOSPHOPROTEIN 1 2 121 0.0000000
4 g5018.t2 PANTHER PTHR22904 TPR REPEAT CONTAINING PROTEIN 2 121 0.0000000
1 g5018.t2 Pfam PF00515 Tetratricopeptide repeat 11 43 0.0000000
2 g5018.t2 Pfam PF17830 STI1 domain 62 114 0.0000000
11 g5018.t2 ProSiteProfiles PS50293 TPR repeat region circular profile. 1 43 10.6080000
10 g5018.t2 ProSiteProfiles PS50005 TPR repeat profile. 10 43 10.1190000
6 g5018.t2 SMART SM00028 tpr_5 10 43 0.0000069
7 g5018.t2 SMART SM00727 CBM 71 110 0.0000000
5 g5018.t2 SUPERFAMILY SSF48452 TPR-like 2 54 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5018/g5018.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5018.t2.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