Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g13545 g13545.t6 TTS g13545.t6 30802222 30802222
chr_1 g13545 g13545.t6 isoform g13545.t6 30802285 30803315
chr_1 g13545 g13545.t6 exon g13545.t6.exon1 30802285 30802608
chr_1 g13545 g13545.t6 cds g13545.t6.CDS1 30802285 30802608
chr_1 g13545 g13545.t6 exon g13545.t6.exon2 30803034 30803117
chr_1 g13545 g13545.t6 cds g13545.t6.CDS2 30803034 30803108
chr_1 g13545 g13545.t6 exon g13545.t6.exon3 30803197 30803315
chr_1 g13545 g13545.t6 TSS g13545.t6 30803370 30803370

Sequences

>g13545.t6 Gene=g13545 Length=527
TCTGTGTTTTTCACTCAATTAAAAAACTCAAAAACTAATTTAATAATAAAACAAACATTT
GTTTTGTTTAATGCATTTGAAGTAATACAAAAATGCATTAAAATAAGACATTTATTTGAA
TCGCCAAAATGCAATTACACATTCGTGGTCAGCAAAACCATGTGTTGGAAGTCCAACCAG
AGGAAACTGTTTCAATTATTAAGGCTAAATTAGCAGTTCTTGAAAATGTTGACATCAATA
CTGAAATGACACTTGCTTGTGAAGGCATTATTCTCGCTGATAACGATACAGTTTCAGAAC
TCAGCAATGTTGAATTAGACCTTACAATCCCACTTCTTGGTGGTAAAGTTCACGGTTCTT
TGGCACGTGCTGGAAAAGTTAAAGGACAAACACCAAAAGTAGAGAAACAGGAAAAGAGAA
AGAAGAAGACAGGACGTGCTAAGAGACGCATTCAATTCAACCGCCGTTTTGCTAATGTTG
TCCAAGGCTTTGGTCGCAAACGTGGACCTAACGCTAATTCCTCATAA

>g13545.t6 Gene=g13545 Length=132
MQLHIRGQQNHVLEVQPEETVSIIKAKLAVLENVDINTEMTLACEGIILADNDTVSELSN
VELDLTIPLLGGKVHGSLARAGKVKGQTPKVEKQEKRKKKTGRAKRRIQFNRRFANVVQG
FGRKRGPNANSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13545.t6 Gene3D G3DSA:3.10.20.90 - 1 104 2.1E-6
7 g13545.t6 MobiDBLite mobidb-lite consensus disorder prediction 81 106 -
3 g13545.t6 PANTHER PTHR12650:SF30 40S RIBOSOMAL PROTEIN S30 2 131 1.1E-42
4 g13545.t6 PANTHER PTHR12650 40S RIBOSOMAL PROTEIN S30/UBIQUITIN-LIKE PROTEIN FUBI 2 131 1.1E-42
2 g13545.t6 Pfam PF00240 Ubiquitin family 8 69 5.1E-7
1 g13545.t6 Pfam PF04758 Ribosomal protein S30 73 130 1.6E-28
9 g13545.t6 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 59 10.419
6 g13545.t6 SMART SM00213 ubq_7 1 72 8.7E-6
5 g13545.t6 SUPERFAMILY SSF54236 Ubiquitin-like 3 94 5.89E-9

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005840 ribosome CC
GO:0005515 protein binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

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