Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L34.

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 g5945 g5945.t2 isoform g5945.t2 12952196 12953636
chr_2 g5945 g5945.t2 exon g5945.t2.exon1 12952196 12952555
chr_2 g5945 g5945.t2 TSS g5945.t2 12952505 12952505
chr_2 g5945 g5945.t2 exon g5945.t2.exon2 12952859 12952933
chr_2 g5945 g5945.t2 cds g5945.t2.CDS1 12952869 12952933
chr_2 g5945 g5945.t2 exon g5945.t2.exon3 12953162 12953636
chr_2 g5945 g5945.t2 cds g5945.t2.CDS2 12953162 12953636
chr_2 g5945 g5945.t2 TTS g5945.t2 12953711 12953711

Sequences

>g5945.t2 Gene=g5945 Length=910
AGTATATTTTTGTCACCAAAATTTTACAACCAAAAGACGAGGATGATTGATAAACAAGAA
AGTTGATTATGATTCAAAGATCAAAATAAACAAGCAGTAAAGTGGAAATGTATTAACCTT
ATTGTGAAATAATAAAATGTAGTTGTTAAAAATCGTAATTAAACCATTCTTATATTTCTT
ATGAAACATAAAAATTGCATTATGAAGCTATTATAGCGATTGACAAGTAAAATAATCGAT
AGTATTCAAGGTTAATTTTGCAAAACTCCTGAAATCAATGAAATCCCGAGCGATGCGACA
TCTACTCTTTCTTTTTTGAACCTTAATTGATTCGGAAGACACGTTTTTTGAATTAAATTG
ATAATTCAATATGGTTCAACGATTAACATTGAGACGACGATTGTCGTATAATACAAAATC
AAACAAACGACGAATTGTTCGTACTCCTGGTGGACGTCTCGTATATCTTTATTTGAAAAA
GAAGCGTACTGTCCCAAGATGTGCAGTAACAAAGGAAAAATTGCACGGTATCACTCCATC
ACGCCCAAGTGAACGTCCTCGTATGGCAAAACGCCTAAAGACAGTCAGACGTGCATATGG
TGGTGTCCTTAGTCACAAAGCTCTTCGTGAACGTATCATTCGTGCATTCTTGATTGATGA
ACAGAAGGTGGTGAAAGTATTGAAGGCTGCTCAAGCAACAACAGTGAAAGCACCAAAACC
ACAAGCTAAACCTAAACCAACTGCAAAACCAGCTGCTCCAGCTCCACAAAAAGGTGGTGC
AAAGGGTGATAAGAAATCTGCTGACAAGAAGAGCGATAAGAAGCCAGTTGCTGCAGACAA
AAAATCAGCCGGAGGAAAGACAGTACCAAAACCATCCGCCGGTGCACCAGCCAAGAAAGC
AAAGAAGTAA

>g5945.t2 Gene=g5945 Length=179
MVQRLTLRRRLSYNTKSNKRRIVRTPGGRLVYLYLKKKRTVPRCAVTKEKLHGITPSRPS
ERPRMAKRLKTVRRAYGGVLSHKALRERIIRAFLIDEQKVVKVLKAAQATTVKAPKPQAK
PKPTAKPAAPAPQKGGAKGDKKSADKKSDKKPVAADKKSAGGKTVPKPSAGAPAKKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5945.t2 Gene3D G3DSA:3.40.1800.40 - 39 120 7.2E-28
10 g5945.t2 MobiDBLite mobidb-lite consensus disorder prediction 110 179 -
9 g5945.t2 MobiDBLite mobidb-lite consensus disorder prediction 138 157 -
2 g5945.t2 PANTHER PTHR10759:SF0 FI02850P-RELATED 1 110 1.4E-43
3 g5945.t2 PANTHER PTHR10759 60S RIBOSOMAL PROTEIN L34 1 110 1.4E-43
5 g5945.t2 PRINTS PR01250 Ribosomal protein L34 signature 13 26 1.5E-26
6 g5945.t2 PRINTS PR01250 Ribosomal protein L34 signature 26 43 1.5E-26
4 g5945.t2 PRINTS PR01250 Ribosomal protein L34 signature 44 54 1.5E-26
7 g5945.t2 PRINTS PR01250 Ribosomal protein L34 signature 64 86 1.5E-26
1 g5945.t2 Pfam PF01199 Ribosomal protein L34e 1 94 3.9E-37
8 g5945.t2 ProSitePatterns PS01145 Ribosomal protein L34e signature. 15 28 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5945/g5945.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5945.t2.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