Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable 39S ribosomal protein L24, mitochondrial.

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 g2257 g2257.t4 TTS g2257.t4 16319728 16319728
chr_3 g2257 g2257.t4 isoform g2257.t4 16319796 16320683
chr_3 g2257 g2257.t4 exon g2257.t4.exon1 16319796 16320301
chr_3 g2257 g2257.t4 cds g2257.t4.CDS1 16319796 16320301
chr_3 g2257 g2257.t4 exon g2257.t4.exon2 16320359 16320683
chr_3 g2257 g2257.t4 cds g2257.t4.CDS2 16320359 16320410
chr_3 g2257 g2257.t4 TSS g2257.t4 16320733 16320733

Sequences

>g2257.t4 Gene=g2257 Length=831
ATGAGAATTACGCTAATAAATCAAGCTAAAAAATACAATATCTTAAAGAATATAGGTGAA
TTGTCAAAAACATATGGAAATTTCCCTGATTCATATGTGAAAAGAGCTTCAGAACAAGTT
TATTGGTAAGTGCCGAAAATTTATTAATTGCTTGATCTAAAATCGTGCTTTTGTTTTAGG
AAAACACCAAGAGCACCTCAATATCAGAAAAGAACGGTAGAGAAGAACAATTTTCGATTT
ACAACCAATCGGCCATGGACAGGACAATTCAAAATGCAAAATATGCCGAATATGAGAAGA
AAAAAAGTTTTCATTGAACCAATTCAGAATTGGAGTTTTTTTAGAGGTGATCGAGTTGAA
GTACTTGTAGGAAAAGATAAAGGAAAGCAAGGAATTATTAATCAAATCTTTCAAGAACGC
AATTGGGTGATTGTTGAAGGTTTAAATTGTCATTTTCGATCAGTGGGAAAGGAAAAAGAT
TATCCAGGGGTTATTATTAGATCAGAAGCACCTCTCTTAGTGACTAGTCAAGTGAAATTA
GTTGATCCAACTGATTTGCTAGCGACAGATATTGAATGGCGATATACAGAAGATGGTGAG
CGTGTAAGAGTGTCAACGAGAACAGGAAGAATTCTTCCTATTCCAAAAGCTCACGAGGAG
ACAATGGATTACAAAGCAAAGAAATTGTATTTAAATAGGGAAAAAGATACCCCAGAAGAT
GTTGTAACTGAAATCACATTCGAACCTAAACTTGCAACTTTTGAAATGGACATAATGGAA
GAAATGAAAATAGAAGAAAATCGTGTGCCAAAGAAGACCTATTGGTACTAA

>g2257.t4 Gene=g2257 Length=185
MQNMPNMRRKKVFIEPIQNWSFFRGDRVEVLVGKDKGKQGIINQIFQERNWVIVEGLNCH
FRSVGKEKDYPGVIIRSEAPLLVTSQVKLVDPTDLLATDIEWRYTEDGERVRVSTRTGRI
LPIPKAHEETMDYKAKKLYLNREKDTPEDVVTEITFEPKLATFEMDIMEEMKIEENRVPK
KTYWY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2257.t4 CDD cd06089 KOW_RPL26 25 89 1.05569E-18
7 g2257.t4 Gene3D G3DSA:2.30.30.30 - 13 120 1.9E-26
5 g2257.t4 Hamap MF_01326_B 50S ribosomal protein L24 [rplX]. 20 116 11.338312
3 g2257.t4 PANTHER PTHR12903 MITOCHONDRIAL RIBOSOMAL PROTEIN L24 8 185 2.0E-50
4 g2257.t4 PANTHER PTHR12903:SF0 39S RIBOSOMAL PROTEIN L24, MITOCHONDRIAL 8 185 2.0E-50
2 g2257.t4 Pfam PF00467 KOW motif 24 55 4.2E-7
1 g2257.t4 Pfam PF17136 Ribosomal proteins 50S L24/mitochondrial 39S L24 58 120 1.8E-11
9 g2257.t4 ProSitePatterns PS01108 Ribosomal protein L24 signature. 25 42 -
10 g2257.t4 SMART SM00739 kow_9 21 48 3.0E-4
6 g2257.t4 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 15 120 2.65E-24
11 g2257.t4 TIGRFAM TIGR01079 rplX_bact: ribosomal protein uL24 24 120 3.7E-20

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:0003723 RNA binding MF
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