Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein lethal(2)essential for life.

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 g5648 g5648.t11 TSS g5648.t11 10883199 10883199
chr_2 g5648 g5648.t11 isoform g5648.t11 10883329 10884280
chr_2 g5648 g5648.t11 exon g5648.t11.exon1 10883329 10883479
chr_2 g5648 g5648.t11 exon g5648.t11.exon2 10883602 10884280
chr_2 g5648 g5648.t11 cds g5648.t11.CDS1 10883626 10884144
chr_2 g5648 g5648.t11 TTS g5648.t11 10884274 10884274

Sequences

>g5648.t11 Gene=g5648 Length=830
ATGGCATTATTACCAGTTTTATTGGACTTAGTCGATGATCTTTATGAGAATCTCGAGAAT
CCATCAAGAAATGAGATTCCATTGCTGTATTTACCTCAAAGAAGTGTGCAAGGAGGCTGC
CCAAGAATGACAAGACGTCATTGCCCAAGAGACCGGCAAATGTCAACGTGAAGGCATGAA
ACAGAAAGACTGGAATGCTTTAGCATTTTATGATCATCCATTAGCTCGTCAGTTCCCTTG
GGAATTATTGAGACACTGTCAAAACCAAAGAGAATGTCCAGTAAAGACACCAGAAGACTT
TGAAGTTATTCTCAATGTGAAATCATTCAAACCAGAAGATATTTCTGTCAAGGTCAAAGG
ACGTGAAATAATTATTGAAGGAAAGCATGAAGAGCGACAAGAAGATAATGGTTTTGTATC
TCGTCAATTTACTCGTCGATATGTTTTGGGTGAAGAATTTGATATTGACACAGTCACTTC
TTATTTGAGTGCAGATGGTCAAATGATCATTAGAGCATTAAAACCAAAACCAGTTTCTCA
AACCACTGAACGAATCATTCCAATTGAGCGTGTTGCTTCAACACCACAACCAAAGAAGGA
TGATGAAAACAAAGGTGAATCTTCATCGGCAATCACTGAGGAAAAGAAAGCAGCTGATTT
CGAGATCGTTGACAATGTCGAGAAGAAGGAATAAATTTTATAATTTTTCTATGGTTATTA
CTCACTATATAAATCAATTATAAAGTATTGTGATTACGTTCCTCTTAGCAATGTAACTCA
TAATTTATTTATTTATGTAATCAATAAAAAAAGCTTGAAGCAATAAAAAA

>g5648.t11 Gene=g5648 Length=172
MKQKDWNALAFYDHPLARQFPWELLRHCQNQRECPVKTPEDFEVILNVKSFKPEDISVKV
KGREIIIEGKHEERQEDNGFVSRQFTRRYVLGEEFDIDTVTSYLSADGQMIIRALKPKPV
SQTTERIIPIERVASTPQPKKDDENKGESSSAITEEKKAADFEIVDNVEKKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5648.t11 CDD cd06526 metazoan_ACD 40 116 5.66515E-34
9 g5648.t11 Gene3D G3DSA:2.60.40.790 - 19 151 1.5E-27
12 g5648.t11 MobiDBLite mobidb-lite consensus disorder prediction 126 172 -
11 g5648.t11 MobiDBLite mobidb-lite consensus disorder prediction 136 172 -
2 g5648.t11 PANTHER PTHR45640 HEAT SHOCK PROTEIN HSP-12.2-RELATED 37 140 1.4E-32
5 g5648.t11 PRINTS PR00299 Alpha crystallin signature 36 56 5.3E-16
6 g5648.t11 PRINTS PR00299 Alpha crystallin signature 58 71 5.3E-16
7 g5648.t11 PRINTS PR00299 Alpha crystallin signature 73 92 5.3E-16
4 g5648.t11 PRINTS PR00299 Alpha crystallin signature 95 116 5.3E-16
3 g5648.t11 PRINTS PR00299 Alpha crystallin signature 125 140 5.3E-16
1 g5648.t11 Pfam PF00011 Hsp20/alpha crystallin family 37 130 2.0E-20
13 g5648.t11 ProSiteProfiles PS01031 Small heat shock protein (sHSP) domain profile. 24 131 15.95
8 g5648.t11 SUPERFAMILY SSF49764 HSP20-like chaperones 36 123 7.67E-14

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5648/g5648.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5648.t11.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed