Gene loci information

Transcript annotation

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

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 g14133 g14133.t19 TTS g14133.t19 34847948 34847948
chr_1 g14133 g14133.t19 isoform g14133.t19 34848031 34849291
chr_1 g14133 g14133.t19 exon g14133.t19.exon1 34848031 34848633
chr_1 g14133 g14133.t19 cds g14133.t19.CDS1 34848031 34848633
chr_1 g14133 g14133.t19 exon g14133.t19.exon2 34848874 34849072
chr_1 g14133 g14133.t19 cds g14133.t19.CDS2 34848874 34849041
chr_1 g14133 g14133.t19 exon g14133.t19.exon3 34849279 34849291
chr_1 g14133 g14133.t19 TSS g14133.t19 34849310 34849310

Sequences

>g14133.t19 Gene=g14133 Length=815
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTG
CCCATATTATTAACTTGGGACGAACATGGGAGATCTATGCTATCTCATCACGAGCTTATG
GACAGCGTGCTGTCTTGAAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTT
TCACTCCTGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGA
TTGTTACTGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTC
CTGTCATTGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCAT
GTAATACAAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTT
TACGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCT
TCTATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAG
TTAAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCG
CAATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGC
AATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t19 Gene=g14133 Length=256
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEIYAI
SSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPRLLIVTDPLSDHQPVTEA
SYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEV
MVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNE
DETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14133.t19 CDD cd01425 RPS2 18 167 9.48627E-62
7 g14133.t19 Gene3D G3DSA:3.40.50.10490 - 14 203 7.9E-91
5 g14133.t19 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 2 252 46.702587
3 g14133.t19 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 249 9.3E-102
4 g14133.t19 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 249 9.3E-102
1 g14133.t19 Pfam PF00318 Ribosomal protein S2 100 165 1.3E-12
2 g14133.t19 Pfam PF16122 40S ribosomal protein SA C-terminus 185 245 8.8E-10
9 g14133.t19 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
10 g14133.t19 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 102 126 -
6 g14133.t19 SUPERFAMILY SSF52313 Ribosomal protein S2 12 183 1.57E-64
11 g14133.t19 TIGRFAM TIGR01012 uS2_euk_arch: ribosomal protein uS2 13 188 2.6E-70

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:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0015935 small ribosomal subunit CC

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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