Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S2.

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 g9524 g9524.t2 isoform g9524.t2 3883095 3889610
chr_1 g9524 g9524.t2 exon g9524.t2.exon1 3883095 3883124
chr_1 g9524 g9524.t2 exon g9524.t2.exon2 3888286 3888673
chr_1 g9524 g9524.t2 cds g9524.t2.CDS1 3888353 3888673
chr_1 g9524 g9524.t2 exon g9524.t2.exon3 3888871 3889289
chr_1 g9524 g9524.t2 cds g9524.t2.CDS2 3888871 3889289
chr_1 g9524 g9524.t2 exon g9524.t2.exon4 3889490 3889610
chr_1 g9524 g9524.t2 cds g9524.t2.CDS3 3889490 3889610
chr_1 g9524 g9524.t2 TSS g9524.t2 3890000 3890000
chr_1 g9524 g9524.t2 TTS g9524.t2 NA NA

Sequences

>g9524.t2 Gene=g9524 Length=958
ATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGGT
GGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGGTGGAAGA
GGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAAAAAGAATGGGTACCAGTC
ACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCATTGGAAGAAATTTACTTG
TACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTCTTGGGACGTTCATTGCGT
GATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGTGCCGGTCAACGTACGCGC
TTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACATTGGTCTTGGTGTAAAATGC
AGCAAAGAAGTCGCCACTGCTATTCGTGGAGCTATCATTTTGGCTAAACTTTCAGTAGTT
CCGGTTCGTCGTGGTTATTGGGGTAACAAAATCGGTAAACCTCATACAGTACCTTGCAAG
GTTACTGGCAAATGTGGTTCAGTTCAAGTCAAATTGATTCCAGCACCAAGAGGAACAGGC
ATTGTTAGTGCTCCAGTTCCAAAGAAATTACTTCAAATGGCTGGTATTGAAGATTGCTAC
ACTCAATGTCGCGGTTCAACTACAACTTTGGGTAACTTCGCAAAAGCCACTTACTCAGCT
ATCATGAAGACTTATGCTTTCTTGACACCTGATTTGTGGAAAGAAATTCCTTTAAGCAAA
TCACCATACGAAGTTTATGCTGACTTCCTTGCGAAACCAGCTGGTAAAACTGGAGGCATT
CGCAACATTGATTTGTCTTAAAATGTTAAAAATGCCCTTTGAAAAACATTCACAAATAAA
ATGACATCCATTTTTAAAGTGATTTATTTTTCACATCTTCATCTCTTTTTCAATGACA

>g9524.t2 Gene=g9524 Length=286
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK
VTGKCGSVQVKLIPAPRGTGIVSAPVPKKLLQMAGIEDCYTQCRGSTTTLGNFAKATYSA
IMKTYAFLTPDLWKEIPLSKSPYEVYADFLAKPAGKTGGIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9524.t2 Gene3D G3DSA:3.30.160.770 - 56 161 1.8E-55
7 g9524.t2 Gene3D G3DSA:3.30.230.10 - 162 255 1.4E-54
10 g9524.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
3 g9524.t2 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 3 273 2.5E-127
4 g9524.t2 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 3 273 2.5E-127
1 g9524.t2 Pfam PF00333 Ribosomal protein S5, N-terminal domain 99 163 6.0E-29
2 g9524.t2 Pfam PF03719 Ribosomal protein S5, C-terminal domain 182 253 1.4E-24
9 g9524.t2 ProSitePatterns PS00585 Ribosomal protein S5 signature. 116 148 -
11 g9524.t2 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 99 162 22.324
6 g9524.t2 SUPERFAMILY SSF54768 dsRNA-binding domain-like 93 164 2.93E-21
5 g9524.t2 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 175 255 2.53E-25
12 g9524.t2 TIGRFAM TIGR01020 uS5_euk_arch: ribosomal protein uS5 53 258 1.7E-95

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:0003723 RNA binding MF
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.

Raw TPM values