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.t5 TTS g2010.t5 14385612 14385612
chr_3 g2010 g2010.t5 isoform g2010.t5 14385683 14386233
chr_3 g2010 g2010.t5 exon g2010.t5.exon1 14385683 14385805
chr_3 g2010 g2010.t5 cds g2010.t5.CDS1 14385683 14385805
chr_3 g2010 g2010.t5 exon g2010.t5.exon2 14385890 14386063
chr_3 g2010 g2010.t5 cds g2010.t5.CDS2 14385890 14386063
chr_3 g2010 g2010.t5 exon g2010.t5.exon3 14386231 14386233
chr_3 g2010 g2010.t5 cds g2010.t5.CDS3 14386231 14386233
chr_3 g2010 g2010.t5 TSS g2010.t5 14386293 14386293

Sequences

>g2010.t5 Gene=g2010 Length=300
ATGGTGAACGTTCCAAAACAACGCAGAACTTATTGCCGTAAATGTAACGCACATCGCGTT
CATAAGGTATCGCAATACAAAAAATCAAAGGAAAGAAAGGCTTCACAAGGTCGTCGTCGT
TACGACAGAAAACAACAAGGTTTTGGTGGTCAAACCAAACCAATTTTCAGAAAGAAGAAA
ATTGTTCTTCGTATGGAATGTACTGAATGCAAATTCCGCAAACAAACACCAATTCGTCGT
TGTAAACATTTTGAATTGGGAGGAGACAAGAAACGCAAGGGACAAATGATTCAGTTCTAA

>g2010.t5 Gene=g2010 Length=99
MVNVPKQRRTYCRKCNAHRVHKVSQYKKSKERKASQGRRRYDRKQQGFGGQTKPIFRKKK
IVLRMECTECKFRKQTPIRRCKHFELGGDKKRKGQMIQF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2010.t5 Gene3D G3DSA:3.10.450.80 - 1 99 2.1E-44
6 g2010.t5 MobiDBLite mobidb-lite consensus disorder prediction 22 55 -
5 g2010.t5 MobiDBLite mobidb-lite consensus disorder prediction 29 46 -
2 g2010.t5 PANTHER PTHR10369:SF3 RIBOSOMAL PROTEIN L36A LIKE 1 99 2.1E-40
3 g2010.t5 PANTHER PTHR10369 60S RIBOSOMAL PROTEIN L36A/L44 1 99 2.1E-40
1 g2010.t5 Pfam PF00935 Ribosomal protein L44 18 86 8.3E-26
4 g2010.t5 SUPERFAMILY SSF57829 Zn-binding ribosomal proteins 2 87 5.68E-31

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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