Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin-40S ribosomal protein S27a.

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 g11608 g11608.t4 TSS g11608.t4 17430574 17430574
chr_1 g11608 g11608.t4 isoform g11608.t4 17430602 17432615
chr_1 g11608 g11608.t4 exon g11608.t4.exon1 17430602 17430604
chr_1 g11608 g11608.t4 exon g11608.t4.exon2 17432150 17432615
chr_1 g11608 g11608.t4 cds g11608.t4.CDS1 17432157 17432615
chr_1 g11608 g11608.t4 TTS g11608.t4 17432683 17432683

Sequences

>g11608.t4 Gene=g11608 Length=469
AAGACACAAGATGCAGATCTTCGTCAAAACACTAACAGGCAAGACCATTACACTTGAGGT
CGAGCCATCTGATACAATCGAAAATGTCAAAGCTAAAATTCAAGACAAAGAAGGCATTCC
TCCAGATCAACAGCGTTTAATCTTTGCTGGTAAACAATTGGAGGATGGACGAACATTGAG
TGATTACAACATTCAAAAAGAATCAACATTGCATTTGGTCCTTCGTCTCCGCGGTGGTGC
CAAAAAACGCAAGAAGAAGAATTACTCAACACCGAAGAAGATCAAGCATAAGCGCAAGAA
GGTTAAACTTGCTGTTTTGAAGTACTACAAAGTTGATGAGAACGGCAAAATCCATCGATT
GAGACGTGAATGCCCGGCAGAAACATGCGGTGCTGGAGTCTTCATGGCAGCACATGAAAA
TCGCGCTTACTGTGGCAAATGTACACTCACATTCGTCGATAAGGAATAA

>g11608.t4 Gene=g11608 Length=152
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKNYSTPKKIKHKRKKVKLAVLKYYKVDENGKIHRLRRE
CPAETCGAGVFMAAHENRAYCGKCTLTFVDKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11608.t4 CDD cd01803 Ubl_ubiquitin 1 76 2.08869E-56
10 g11608.t4 Gene3D G3DSA:3.10.20.90 - 1 77 8.2E-45
11 g11608.t4 Gene3D G3DSA:2.20.25.660 - 79 152 9.5E-38
3 g11608.t4 PANTHER PTHR10666 UBIQUITIN 1 148 5.9E-89
4 g11608.t4 PANTHER PTHR10666:SF291 - 1 148 5.9E-89
7 g11608.t4 PRINTS PR00348 Ubiquitin signature 11 31 4.6E-39
6 g11608.t4 PRINTS PR00348 Ubiquitin signature 32 52 4.6E-39
5 g11608.t4 PRINTS PR00348 Ubiquitin signature 53 74 4.6E-39
2 g11608.t4 Pfam PF00240 Ubiquitin family 3 74 2.3E-34
1 g11608.t4 Pfam PF01599 Ribosomal protein S27a 102 147 1.2E-24
13 g11608.t4 ProSitePatterns PS00299 Ubiquitin domain signature. 27 52 -
16 g11608.t4 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 76 31.018
15 g11608.t4 SMART SM00213 ubq_7 1 72 2.9E-36
14 g11608.t4 SMART SM01402 Ribosomal_S27_2 102 147 3.7E-27
9 g11608.t4 SUPERFAMILY SSF54236 Ubiquitin-like 1 93 2.75E-36
8 g11608.t4 SUPERFAMILY SSF57829 Zn-binding ribosomal proteins 100 150 1.83E-18

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