Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L44.

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_3 g2010 g2010.t6 TTS g2010.t6 14385612 14385612
chr_3 g2010 g2010.t6 isoform g2010.t6 14385683 14388607
chr_3 g2010 g2010.t6 exon g2010.t6.exon1 14385683 14385820
chr_3 g2010 g2010.t6 cds g2010.t6.CDS1 14385683 14385820
chr_3 g2010 g2010.t6 exon g2010.t6.exon2 14385890 14386063
chr_3 g2010 g2010.t6 cds g2010.t6.CDS2 14385890 14386063
chr_3 g2010 g2010.t6 exon g2010.t6.exon3 14386231 14386285
chr_3 g2010 g2010.t6 cds g2010.t6.CDS3 14386231 14386233
chr_3 g2010 g2010.t6 exon g2010.t6.exon4 14388592 14388607
chr_3 g2010 g2010.t6 TSS g2010.t6 NA NA

Sequences

>g2010.t6 Gene=g2010 Length=383
TTGTTCTTCGTTCAGTCTGAAAACACAAAAAATCGTGTTGAAGTTTTTGAGTTTCTTCAG
AAAATAAAATGGTGAACGTTCCAAAACAACGCAGAACTTATTGCCGTAAATGTAACGCAC
ATCGCGTTCATAAGGTATCGCAATACAAAAAATCAAAGGAAAGAAAGGCTTCACAAGGTC
GTCGTCGTTACGACAGAAAACAACAAGGTTTTGGTGGTCAAACCAAACCAATTTTCAGAA
AGAAGGCCAAAACTACCAAGAAAATTGTTCTTCGTATGGAATGTACTGAATGCAAATTCC
GCAAACAAACACCAATTCGTCGTTGTAAACATTTTGAATTGGGAGGAGACAAGAAACGCA
AGGGACAAATGATTCAGTTCTAA

>g2010.t6 Gene=g2010 Length=104
MVNVPKQRRTYCRKCNAHRVHKVSQYKKSKERKASQGRRRYDRKQQGFGGQTKPIFRKKA
KTTKKIVLRMECTECKFRKQTPIRRCKHFELGGDKKRKGQMIQF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2010.t6 Gene3D G3DSA:3.10.450.80 - 1 104 9.8E-51
4 g2010.t6 Hamap MF_01476 50S ribosomal protein L44e [rpl44e]. 2 92 19.04797
8 g2010.t6 MobiDBLite mobidb-lite consensus disorder prediction 22 61 -
7 g2010.t6 MobiDBLite mobidb-lite consensus disorder prediction 29 46 -
2 g2010.t6 PANTHER PTHR10369:SF3 RIBOSOMAL PROTEIN L36A LIKE 1 104 6.6E-47
3 g2010.t6 PANTHER PTHR10369 60S RIBOSOMAL PROTEIN L36A/L44 1 104 6.6E-47
1 g2010.t6 Pfam PF00935 Ribosomal protein L44 18 91 1.8E-31
6 g2010.t6 ProSitePatterns PS01172 Ribosomal protein L44e signature. 61 72 -
5 g2010.t6 SUPERFAMILY SSF57829 Zn-binding ribosomal proteins 2 92 2.01E-34

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: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