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.t39 TTS g9524.t39 3888292 3888292
chr_1 g9524 g9524.t39 isoform g9524.t39 3888296 3889977
chr_1 g9524 g9524.t39 exon g9524.t39.exon1 3888296 3888495
chr_1 g9524 g9524.t39 cds g9524.t39.CDS1 3888462 3888495
chr_1 g9524 g9524.t39 exon g9524.t39.exon2 3888827 3889289
chr_1 g9524 g9524.t39 cds g9524.t39.CDS2 3888827 3889289
chr_1 g9524 g9524.t39 exon g9524.t39.exon3 3889490 3889611
chr_1 g9524 g9524.t39 cds g9524.t39.CDS3 3889490 3889610
chr_1 g9524 g9524.t39 exon g9524.t39.exon4 3889961 3889977
chr_1 g9524 g9524.t39 TSS g9524.t39 3890000 3890000

Sequences

>g9524.t39 Gene=g9524 Length=802
CAAAAGACACGAAAGATAATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGT
TTCGGAGGTGCAGCTGGTGGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGC
GGAGGTCGCGGTGGAAGAGGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAA
AAAGAATGGGTACCAGTCACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCA
TTGGAAGAAATTTACTTGTACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTC
TTGGGACGTTCATTGCGTGATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGT
GCCGGTCAACGTACGCGCTTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACATT
GGTCTTGGTGTAAAATGCAGCAAAGAAGTCGCCACTGCTATTCGTGGAGCTATCATTTTG
GCTAAACTTTCAGTAGTTCCGGTTCGTCGTGGTTATTGGGGTAACAAAATCGGTAAACCT
CATACAGTACCTTGCAAGGTAAGAAAATTAATTATAATTTTATTATTAAGAAGGAAAATT
TTCTATCATGAAGACTTATGCTTTCTTGACACCTGATTTGTGGAAAGAAATTCCTTTAAG
CAAATCACCATACGAAGTTTATGCTGACTTCCTTGCGAAACCAGCTGGTAAAACTGGAGG
CATTCGCAACATTGATTTGTCTTAAAATGTTAAAAATGCCCTTTGAAAAACATTCACAAA
TAAAATGACATCCATTTTTAAA

>g9524.t39 Gene=g9524 Length=205
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK
VRKLIIILLLRRKIFYHEDLCFLDT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9524.t39 Gene3D G3DSA:3.30.160.770 - 56 161 8.0E-56
5 g9524.t39 Gene3D G3DSA:3.30.230.10 - 162 192 3.2E-7
8 g9524.t39 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
2 g9524.t39 PANTHER PTHR13718:SF99 GENE 8225-RELATED 17 185 4.8E-80
3 g9524.t39 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 17 185 4.8E-80
1 g9524.t39 Pfam PF00333 Ribosomal protein S5, N-terminal domain 99 163 3.3E-29
7 g9524.t39 ProSitePatterns PS00585 Ribosomal protein S5 signature. 116 148 -
9 g9524.t39 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 99 162 22.324
4 g9524.t39 SUPERFAMILY SSF54768 dsRNA-binding domain-like 93 164 1.57E-21
10 g9524.t39 TIGRFAM TIGR01020 uS5_euk_arch: ribosomal protein uS5 53 182 4.8E-58

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

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