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.t33 TTS g14133.t33 34847948 34847948
chr_1 g14133 g14133.t33 isoform g14133.t33 34848031 34849386
chr_1 g14133 g14133.t33 exon g14133.t33.exon1 34848031 34848633
chr_1 g14133 g14133.t33 cds g14133.t33.CDS1 34848031 34848633
chr_1 g14133 g14133.t33 exon g14133.t33.exon2 34848823 34849031
chr_1 g14133 g14133.t33 cds g14133.t33.CDS2 34848823 34848990
chr_1 g14133 g14133.t33 exon g14133.t33.exon3 34849291 34849386
chr_1 g14133 g14133.t33 TSS g14133.t33 NA NA

Sequences

>g14133.t33 Gene=g14133 Length=908
TAATTTTAAAACTTTATTTTCAATCTCGTGTTTTTGTTTTTGAATTTATTTACAAATTCG
CTCTACTGAATTCGCCCTTTTTCAACTCGCTCTCAAGACTTGATGTACTCGCTTTGCGCG
ATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCGGTTCAGAGCATGTTAATT
TCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTGCCCATATTATTAACTTGG
GACGAACATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTGCTGCTATTGAACATCCAC
AAGAGATCTATGCTATCTCATCACGAGCTTATGGACAGCGTGCTGTCTTGAAATTTGCTC
ATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCCTGGTGCATTCACCAATCAGC
AACAAACAACTTTCCGTGAACCACGTCTATTGATTGTTACTGACCCATTGTCAGATCATC
AGCCAGTCACTGAAGCTTCATATGTCAATATTCCTGTCATTGCTTTTTGCAATACTGACA
GTCCATTGAAATATGTCGATATTGCAATTCCATGTAATACAAAATCGACTCACTCAATTG
GTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCCACGTG
AACAACCATGGGAAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGCTGAAA
AGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATATTGCTG
AAGATCCAACTTATCCAGATGATCCATCAGGCGCAATTATTCCTACACCAGCAGTTGCAA
CAGAAGATTGGAATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAACTCTG
GCTTCTAA

>g14133.t33 Gene=g14133 Length=256
MLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLLAARAIAAIEHPQEIYAI
SSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPRLLIVTDPLSDHQPVTEA
SYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEV
MVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNE
DETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g14133.t33 CDD cd01425 RPS2 1 167 7.79973E-62
13 g14133.t33 Gene3D G3DSA:3.40.50.10490 - 1 203 1.1E-103
6 g14133.t33 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 1 252 49.947865
4 g14133.t33 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 1 249 9.4E-114
5 g14133.t33 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 1 249 9.4E-114
11 g14133.t33 PRINTS PR00395 Ribosomal protein S2 signature 28 37 2.3E-26
10 g14133.t33 PRINTS PR00395 Ribosomal protein S2 signature 77 94 2.3E-26
9 g14133.t33 PRINTS PR00395 Ribosomal protein S2 signature 102 119 2.3E-26
7 g14133.t33 PRINTS PR00395 Ribosomal protein S2 signature 119 130 2.3E-26
8 g14133.t33 PRINTS PR00395 Ribosomal protein S2 signature 140 154 2.3E-26
1 g14133.t33 Pfam PF00318 Ribosomal protein S2 1 96 1.4E-10
2 g14133.t33 Pfam PF00318 Ribosomal protein S2 100 165 1.3E-12
3 g14133.t33 Pfam PF16122 40S ribosomal protein SA C-terminus 185 245 8.8E-10
15 g14133.t33 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 102 126 -
12 g14133.t33 SUPERFAMILY SSF52313 Ribosomal protein S2 1 183 1.31E-70
16 g14133.t33 TIGRFAM TIGR01012 uS2_euk_arch: ribosomal protein uS2 1 188 6.7E-84

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

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