Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L9.

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_2 g5231 g5231.t34 TTS g5231.t34 7931500 7931500
chr_2 g5231 g5231.t34 isoform g5231.t34 7931553 7933195
chr_2 g5231 g5231.t34 exon g5231.t34.exon1 7931553 7931881
chr_2 g5231 g5231.t34 cds g5231.t34.CDS1 7931553 7931881
chr_2 g5231 g5231.t34 exon g5231.t34.exon2 7931953 7932196
chr_2 g5231 g5231.t34 cds g5231.t34.CDS2 7931953 7932193
chr_2 g5231 g5231.t34 exon g5231.t34.exon3 7932418 7932465
chr_2 g5231 g5231.t34 exon g5231.t34.exon4 7933131 7933195
chr_2 g5231 g5231.t34 TSS g5231.t34 NA NA

Sequences

>g5231.t34 Gene=g5231 Length=686
TCTACAGAGTAGATTTTCCATTTTTTCTTTCTTGATTCGAATTTATATTCGAAATTATCA
GAAAAAATCTTTCTTTTTTATTCGATCTCTGTGAAGAGCATTAATTTTTCGAGATCATGA
GAACTATCAACAGCAATCAAGTTGTTAAGCTTCCAAAAGGCGTTGGCGCAAAAGTCAATG
CTCGCGTTATTACAATTCGAGGGCCAAGAGGCAAATTGACTCGCGATTTCCGTCACTTAG
CAATGGATATTCGTATGATCAATCGCAAGAAGATTATGGTTGAGAAGTGGTTCGGAGCTA
AAAAAGAAATTGCTGCTGTAAGAACTGTTTGCAGTCATATCGAAAATATGATCAAGGTTA
CAAAGGGATTCCAATATAAAATGAGAGCTGTACATGCGCATTTTCCCATCAACTGTGTTG
TGTCAGAAAATAATACTGTTATTGAAATCCGTAACTTCTTGGGTGAAAAGCACATTCGTA
AAGTAACAATGAAACCAGGTGTTACAGTTGTCAACTCAGCTAAGCAAAAGGATGAATTGA
TCCTTGAAGGAAATGATATCGAAGCAGTTTCACTATCTGCTGCTCTTATTCAACAATCAA
CAACAGTTAAAAATAAGGATATTCGTAAATTCCTTGACGGTTTGTATGTCTCAGAGAAGA
CTACTGTGGTACAAGAAGAAGAATAA

>g5231.t34 Gene=g5231 Length=189
MRTINSNQVVKLPKGVGAKVNARVITIRGPRGKLTRDFRHLAMDIRMINRKKIMVEKWFG
AKKEIAAVRTVCSHIENMIKVTKGFQYKMRAVHAHFPINCVVSENNTVIEIRNFLGEKHI
RKVTMKPGVTVVNSAKQKDELILEGNDIEAVSLSAALIQQSTTVKNKDIRKFLDGLYVSE
KTTVVQEEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5231.t34 Coils Coil Coil 184 189 -
8 g5231.t34 Gene3D G3DSA:3.90.930.12 - 1 84 2.5E-30
9 g5231.t34 Gene3D G3DSA:3.90.930.12 - 85 189 5.0E-45
3 g5231.t34 PANTHER PTHR11655:SF16 60S RIBOSOMAL PROTEIN L9-RELATED 1 187 5.8E-78
4 g5231.t34 PANTHER PTHR11655 60S/50S RIBOSOMAL PROTEIN L6/L9 1 187 5.8E-78
11 g5231.t34 PIRSF PIRSF002162 RPL6p_RPL6a_RPL9e_RPL9o 1 183 1.1E-33
1 g5231.t34 Pfam PF00347 Ribosomal protein L6 13 81 1.2E-12
2 g5231.t34 Pfam PF00347 Ribosomal protein L6 96 175 4.2E-16
7 g5231.t34 ProSitePatterns PS00700 Ribosomal protein L6 signature 2. 160 181 -
5 g5231.t34 SUPERFAMILY SSF56053 Ribosomal protein L6 1 80 1.37E-18
6 g5231.t34 SUPERFAMILY SSF56053 Ribosomal protein L6 85 181 1.92E-28

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5231/g5231.t34; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5231.t34.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0019843 rRNA binding 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. There were no conditions that were differentially expressed