Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L27a.

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 g10569 g10569.t11 TTS g10569.t11 10486114 10486114
chr_1 g10569 g10569.t11 isoform g10569.t11 10486175 10487149
chr_1 g10569 g10569.t11 exon g10569.t11.exon1 10486175 10486303
chr_1 g10569 g10569.t11 cds g10569.t11.CDS1 10486175 10486303
chr_1 g10569 g10569.t11 exon g10569.t11.exon2 10486505 10486752
chr_1 g10569 g10569.t11 cds g10569.t11.CDS2 10486505 10486752
chr_1 g10569 g10569.t11 exon g10569.t11.exon3 10486848 10486914
chr_1 g10569 g10569.t11 cds g10569.t11.CDS3 10486848 10486908
chr_1 g10569 g10569.t11 exon g10569.t11.exon4 10487006 10487149
chr_1 g10569 g10569.t11 TSS g10569.t11 10487169 10487169

Sequences

>g10569.t11 Gene=g10569 Length=588
ATGGTTGTGAGTAAAATTTTTAATTTTAATAAAATTAAATAGTATCAATGACTTTTTTAA
GATAAATAGTAATTTATTCTAATTGCCATATTATGAATTACTATTAGCATATGAAGAATT
TTAGTTAGACTTTGATAAAACTATAGTCTTATGAAAAGAAAGAAGACCCGAAAGCTTCGT
GGTCATGTCAGCCATGGTCATGGTCGTATCGGCAAACACAGAAAACATCCTGGTGGTCGC
GGTAATGCTGGTGGTATGCACCATCACAGAATAAATTACGATAAATACCATCCTGGATAT
TTTGGAAAAGTTGGTATGCGCAACTTCCATTTGAATCGTAATCACAGCTTCTGTCCAACA
ATTAATCTCGATAAACTTTGGTCATTAATTGGACAAGAAAATTACGAGAAAGCAAAGAAA
GAAGGCGATAAAGTTCCAGTTATCGATATCGTACAATTTGGATACTTTAAGCTACTTGGA
CATGGACATTTGCCAAAACAACCAATAATTGTGAAAGCAAAATATTTTTCACAGAAAGCA
GAAAAGAAAATCAAGGCTGCTGGTGGCGCATGCATCCTAAGAGCATAA

>g10569.t11 Gene=g10569 Length=145
MKRKKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINYDKYHPGYFGKVGMRNFH
LNRNHSFCPTINLDKLWSLIGQENYEKAKKEGDKVPVIDIVQFGYFKLLGHGHLPKQPII
VKAKYFSQKAEKKIKAAGGACILRA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10569.t11 Gene3D G3DSA:3.100.10.10 - 56 145 5.9E-40
4 g10569.t11 Hamap MF_01341 50S ribosomal protein L15 [rplO]. 1 144 11.601554
7 g10569.t11 MobiDBLite mobidb-lite consensus disorder prediction 1 32 -
2 g10569.t11 PANTHER PTHR11721 60S RIBOSOMAL PROTEIN L27A 2 144 3.5E-65
3 g10569.t11 PANTHER PTHR11721:SF13 60S RIBOSOMAL PROTEIN L27A 2 144 3.5E-65
1 g10569.t11 Pfam PF00828 Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A 26 142 2.1E-23
6 g10569.t11 ProSitePatterns PS00475 Ribosomal protein L15 signature. 107 138 -
5 g10569.t11 SUPERFAMILY SSF52080 Ribosomal proteins L15p and L18e 3 143 4.06E-44

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:0015934 large ribosomal subunit CC
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