Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 40S ribosomal protein S10b.

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_1 g9278 g9278.t4 isoform g9278.t4 1398731 1399725
chr_1 g9278 g9278.t4 exon g9278.t4.exon1 1398731 1398781
chr_1 g9278 g9278.t4 TSS g9278.t4 1398732 1398732
chr_1 g9278 g9278.t4 exon g9278.t4.exon2 1399146 1399345
chr_1 g9278 g9278.t4 cds g9278.t4.CDS1 1399146 1399345
chr_1 g9278 g9278.t4 exon g9278.t4.exon3 1399400 1399725
chr_1 g9278 g9278.t4 cds g9278.t4.CDS2 1399400 1399724
chr_1 g9278 g9278.t4 TTS g9278.t4 1399800 1399800

Sequences

>g9278.t4 Gene=g9278 Length=577
TTCTTTTTCTTCGTGAATATCAAAACGTGAAGATATTCAAAGTAATTCAAAATGTTTATG
CCAAAAGCACATAAAGTGGCGATCTATGAACATCTCTTCAAAGAAGGAGTTCTTGTTGCA
CAAAAGGATTTTCATGCACCAAAACATCCCGAACTCGAGAGCGTTCCAAATCTTCATGTA
ATTAAGACTATGCAGTCATTGAAATCAAGAAATCTTGTTAAGGAACAATTTGCATGGAGA
CATTATTACTGGTATCTCACAAATGAAGGCATTGAATATTTGCGTCAATATCTTCATTTG
CCACCAGAAATCGTTCCATCAACATTGAAGCGAACAACTCGCTCAGATGCTGCTCGTCCT
CGCGCTGCTCCACGTTCAGATGGACCAAAATCAGGAGAAGATCGTCAAGCATACAGACGT
GCACCAGGGCAATCGTCAGACAAAAAAGCCGATGTTGGTGCTGGTGCAGCTGATATTGAA
TTGGTATGTTATAACAAATTTTTTTATTATATCAAATTTAACATATCTTATTTTTTAGCG
TGGTGGATTCGGTCGTGGCTCAAGAGGCCCACAGTAA

>g9278.t4 Gene=g9278 Length=175
MFMPKAHKVAIYEHLFKEGVLVAQKDFHAPKHPELESVPNLHVIKTMQSLKSRNLVKEQF
AWRHYYWYLTNEGIEYLRQYLHLPPEIVPSTLKRTTRSDAARPRAAPRSDGPKSGEDRQA
YRRAPGQSSDKKADVGAGAADIELVCYNKFFYYIKFNISYFLAWWIRSWLKRPTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g9278.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 107 4.5E-50
4 g9278.t4 MobiDBLite mobidb-lite consensus disorder prediction 92 132 -
3 g9278.t4 MobiDBLite mobidb-lite consensus disorder prediction 97 129 -
2 g9278.t4 PANTHER PTHR12146 40S RIBOSOMAL PROTEIN S10 1 139 7.8E-58
1 g9278.t4 Pfam PF03501 Plectin/S10 domain 3 95 3.9E-46
7 g9278.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 149 -
8 g9278.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 170 -
6 g9278.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 171 175 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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