Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L31.

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 g5932 g5932.t4 isoform g5932.t4 12892708 12895485
chr_2 g5932 g5932.t4 exon g5932.t4.exon1 12892708 12893084
chr_2 g5932 g5932.t4 exon g5932.t4.exon2 12894627 12894677
chr_2 g5932 g5932.t4 TSS g5932.t4 12894648 12894648
chr_2 g5932 g5932.t4 exon g5932.t4.exon3 12895045 12895274
chr_2 g5932 g5932.t4 cds g5932.t4.CDS1 12895051 12895274
chr_2 g5932 g5932.t4 exon g5932.t4.exon4 12895338 12895485
chr_2 g5932 g5932.t4 cds g5932.t4.CDS2 12895338 12895485
chr_2 g5932 g5932.t4 TTS g5932.t4 12895626 12895626

Sequences

>g5932.t4 Gene=g5932 Length=806
GTTTTGCAGATGATGGTTCTTTATTTTCTTTATTATCGTATGATGGTGAAAGTATAAATG
AACCGCTCGATGCATTAGTAGGAGTTTGAAGAACAGCGAATGATGAGCTTAAAAGATTAT
TTGGACTATTGGGAGCTTTTGTGAAATATGTTTGTGTTCCTGTCGTTGCATATTTATGAT
GCAACGCATGATGATGAGCAACAATTGGACTAAATGGAGGCGGTGAAGTTGCGATTGATT
TATAAATTTTTTGTGATTGCTCCTCTCTTGGTTGTACGCAATGCACTTCTTCCTGTAATA
ATGAGAGCGATGATGACGAAGAGGCGACTTGTTGTATTTGTGATGACAACTCAGATGATA
ATATTTGAGGTTGAATAGAAATTTCGAAAAGAACTCTTTCTTTTTTCTCTAACAAACTCA
CACGTTTGATAGAAATGGCGAAGGGTAAAACAGAAAAGCGTACCAAATCGGCAATCAATG
AAGTTGTGACACGAGAGTGCACAATTCATCTGAATAAGCGACTCCACAAAGTTGGTTTTA
AAAAACGTTCACCAAGAGCAGTTAAGATCATTCGTAAATTTGCTGAAAAGGAAATGGGAA
CAAAAGATGTGAGAATTGATACCCGTCTTAATAAAGCAATTTGGTCTCGCGGTATCAGAA
ATCCACCTTTCCGCATTCGTGTTCGACTTGCTCGCCGCCGTAATGATGATGAAGATTCAC
CTAACAAGCTTTATACTTTGGTCACATACGTCCCAGTGGAAAGCTTCAAAGAACTCCAAA
CAGAAAATGTTGAATCAGAAGATTAA

>g5932.t4 Gene=g5932 Length=123
MAKGKTEKRTKSAINEVVTRECTIHLNKRLHKVGFKKRSPRAVKIIRKFAEKEMGTKDVR
IDTRLNKAIWSRGIRNPPFRIRVRLARRRNDDEDSPNKLYTLVTYVPVESFKELQTENVE
SED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5932.t4 CDD cd00463 Ribosomal_L31e 14 97 1.29815E-27
6 g5932.t4 Gene3D G3DSA:3.10.440.10 - 1 122 1.6E-56
4 g5932.t4 Hamap MF_00410 50S ribosomal protein L31e [rpl31e]. 15 109 15.773115
2 g5932.t4 PANTHER PTHR10956:SF4 60S RIBOSOMAL PROTEIN L31 3 121 2.4E-55
3 g5932.t4 PANTHER PTHR10956 60S RIBOSOMAL PROTEIN L31 3 121 2.4E-55
1 g5932.t4 Pfam PF01198 Ribosomal protein L31e 16 97 9.5E-44
8 g5932.t4 ProSitePatterns PS01144 Ribosomal protein L31e signature. 59 73 -
9 g5932.t4 SMART SM01380 Ribosomal_L31e_2 15 98 1.8E-54
5 g5932.t4 SUPERFAMILY SSF54575 Ribosomal protein L31e 16 98 1.83E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5932/g5932.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5932.t4.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

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