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.t2 isoform g5648.t2 10874192 10884280
chr_2 g5648 g5648.t2 exon g5648.t2.exon1 10874192 10874197
chr_2 g5648 g5648.t2 TSS g5648.t2 10883199 10883199
chr_2 g5648 g5648.t2 exon g5648.t2.exon2 10883305 10884280
chr_2 g5648 g5648.t2 cds g5648.t2.CDS1 10883329 10884144
chr_2 g5648 g5648.t2 TTS g5648.t2 10884274 10884274

Sequences

>g5648.t2 Gene=g5648 Length=982
ATTGAAAATTAAAAAAAGAATAAAGTAAAAATGGCATTATTACCAGTTTTATTGGACTTA
GTCGATGATCTTTATGAGAATCTCGAGAATCCATCAAGAAATGAGATTCCATTGCTGTAT
TTACCTCAAAGAAGTGTGCAAGGAGGCTGCCCAAGAATGACAAGACGTCATTGCCCAAGA
GGTGATGCAAAAGAATGCCCAGCTAAAGCAGACATGGAAAAGAAAGAAGAAATTAAAGAA
AATCAACAATCTGTGCCATCAGAAGGTTGCCCAAAAGCTTGTACAAGAGGACAATGTCAA
AAGACCGGCAAATGTCAACGTGAAGGCATGAAACAGAAAGACTGGAATGCTTTAGCATTT
TATGATCATCCATTAGCTCGTCAGTTCCCTTGGGAATTATTGAGACACTGTCAAAACCAA
AGAGAATGTCCAGTAAAGACACCAGAAGACTTTGAAGTTATTCTCAATGTGAAATCATTC
AAACCAGAAGATATTTCTGTCAAGGTCAAAGGACGTGAAATAATTATTGAAGGAAAGCAT
GAAGAGCGACAAGAAGATAATGGTTTTGTATCTCGTCAATTTACTCGTCGATATGTTTTG
GGTGAAGAATTTGATATTGACACAGTCACTTCTTATTTGAGTGCAGATGGTCAAATGATC
ATTAGAGCATTAAAACCAAAACCAGTTTCTCAAACCACTGAACGAATCATTCCAATTGAG
CGTGTTGCTTCAACACCACAACCAAAGAAGGATGATGAAAACAAAGGTGAATCTTCATCG
GCAATCACTGAGGAAAAGAAAGCAGCTGATTTCGAGATCGTTGACAATGTCGAGAAGAAG
GAATAAATTTTATAATTTTTCTATGGTTATTACTCACTATATAAATCAATTATAAAGTAT
TGTGATTACGTTCCTCTTAGCAATGTAACTCATAATTTATTTATTTATGTAATCAATAAA
AAAAGCTTGAAGCAATAAAAAA

>g5648.t2 Gene=g5648 Length=271
MALLPVLLDLVDDLYENLENPSRNEIPLLYLPQRSVQGGCPRMTRRHCPRGDAKECPAKA
DMEKKEEIKENQQSVPSEGCPKACTRGQCQKTGKCQREGMKQKDWNALAFYDHPLARQFP
WELLRHCQNQRECPVKTPEDFEVILNVKSFKPEDISVKVKGREIIIEGKHEERQEDNGFV
SRQFTRRYVLGEEFDIDTVTSYLSADGQMIIRALKPKPVSQTTERIIPIERVASTPQPKK
DDENKGESSSAITEEKKAADFEIVDNVEKKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5648.t2 CDD cd06526 metazoan_ACD 139 215 2.59044E-34
9 g5648.t2 Gene3D G3DSA:2.60.40.790 - 118 250 5.1E-27
11 g5648.t2 MobiDBLite mobidb-lite consensus disorder prediction 225 271 -
12 g5648.t2 MobiDBLite mobidb-lite consensus disorder prediction 235 271 -
2 g5648.t2 PANTHER PTHR45640 HEAT SHOCK PROTEIN HSP-12.2-RELATED 83 239 8.4E-33
4 g5648.t2 PRINTS PR00299 Alpha crystallin signature 135 155 3.0E-15
3 g5648.t2 PRINTS PR00299 Alpha crystallin signature 157 170 3.0E-15
7 g5648.t2 PRINTS PR00299 Alpha crystallin signature 172 191 3.0E-15
6 g5648.t2 PRINTS PR00299 Alpha crystallin signature 194 215 3.0E-15
5 g5648.t2 PRINTS PR00299 Alpha crystallin signature 224 239 3.0E-15
1 g5648.t2 Pfam PF00011 Hsp20/alpha crystallin family 136 229 6.0E-20
13 g5648.t2 ProSiteProfiles PS01031 Small heat shock protein (sHSP) domain profile. 123 230 15.95
8 g5648.t2 SUPERFAMILY SSF49764 HSP20-like chaperones 135 221 2.44E-13

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5648/g5648.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5648.t2.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.

Raw TPM values