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.t9 TSS g5648.t9 10883199 10883199
chr_2 g5648 g5648.t9 isoform g5648.t9 10883329 10884144
chr_2 g5648 g5648.t9 exon g5648.t9.exon1 10883329 10883611
chr_2 g5648 g5648.t9 cds g5648.t9.CDS1 10883329 10883611
chr_2 g5648 g5648.t9 exon g5648.t9.exon2 10883654 10884144
chr_2 g5648 g5648.t9 cds g5648.t9.CDS2 10883654 10884144
chr_2 g5648 g5648.t9 TTS g5648.t9 10884274 10884274

Sequences

>g5648.t9 Gene=g5648 Length=774
ATGGCATTATTACCAGTTTTATTGGACTTAGTCGATGATCTTTATGAGAATCTCGAGAAT
CCATCAAGAAATGAGATTCCATTGCTGTATTTACCTCAAAGAAGTGTGCAAGGAGGCTGC
CCAAGAATGACAAGACGTCATTGCCCAAGAGGTGATGCAAAAGAATGCCCAGCTAAAGCA
GACATGGAAAAGAAAGAAGAAATTAAAGAAAATCAACAATCTGTGCCATCAGAAGGTTGC
CCAAAAGCTTGTACAAGAGGACAATGTCAAAAGACCGGCAAATCATTTTATGATCATCCA
TTAGCTCGTCAGTTCCCTTGGGAATTATTGAGACACTGTCAAAACCAAAGAGAATGTCCA
GTAAAGACACCAGAAGACTTTGAAGTTATTCTCAATGTGAAATCATTCAAACCAGAAGAT
ATTTCTGTCAAGGTCAAAGGACGTGAAATAATTATTGAAGGAAAGCATGAAGAGCGACAA
GAAGATAATGGTTTTGTATCTCGTCAATTTACTCGTCGATATGTTTTGGGTGAAGAATTT
GATATTGACACAGTCACTTCTTATTTGAGTGCAGATGGTCAAATGATCATTAGAGCATTA
AAACCAAAACCAGTTTCTCAAACCACTGAACGAATCATTCCAATTGAGCGTGTTGCTTCA
ACACCACAACCAAAGAAGGATGATGAAAACAAAGGTGAATCTTCATCGGCAATCACTGAG
GAAAAGAAAGCAGCTGATTTCGAGATCGTTGACAATGTCGAGAAGAAGGAATAA

>g5648.t9 Gene=g5648 Length=257
MALLPVLLDLVDDLYENLENPSRNEIPLLYLPQRSVQGGCPRMTRRHCPRGDAKECPAKA
DMEKKEEIKENQQSVPSEGCPKACTRGQCQKTGKSFYDHPLARQFPWELLRHCQNQRECP
VKTPEDFEVILNVKSFKPEDISVKVKGREIIIEGKHEERQEDNGFVSRQFTRRYVLGEEF
DIDTVTSYLSADGQMIIRALKPKPVSQTTERIIPIERVASTPQPKKDDENKGESSSAITE
EKKAADFEIVDNVEKKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5648.t9 CDD cd06526 metazoan_ACD 125 201 5.37676E-34
9 g5648.t9 Gene3D G3DSA:2.60.40.790 - 104 236 4.5E-27
11 g5648.t9 MobiDBLite mobidb-lite consensus disorder prediction 211 257 -
12 g5648.t9 MobiDBLite mobidb-lite consensus disorder prediction 221 257 -
2 g5648.t9 PANTHER PTHR45640 HEAT SHOCK PROTEIN HSP-12.2-RELATED 70 225 6.4E-33
7 g5648.t9 PRINTS PR00299 Alpha crystallin signature 121 141 2.4E-15
6 g5648.t9 PRINTS PR00299 Alpha crystallin signature 143 156 2.4E-15
4 g5648.t9 PRINTS PR00299 Alpha crystallin signature 158 177 2.4E-15
3 g5648.t9 PRINTS PR00299 Alpha crystallin signature 180 201 2.4E-15
5 g5648.t9 PRINTS PR00299 Alpha crystallin signature 210 225 2.4E-15
1 g5648.t9 Pfam PF00011 Hsp20/alpha crystallin family 122 215 5.3E-20
13 g5648.t9 ProSiteProfiles PS01031 Small heat shock protein (sHSP) domain profile. 109 216 15.95
8 g5648.t9 SUPERFAMILY SSF49764 HSP20-like chaperones 121 207 2.2E-13

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5648/g5648.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5648.t9.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