Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 39S ribosomal protein L4, 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_2 g8372 g8372.t11 TTS g8372.t11 30059447 30059447
chr_2 g8372 g8372.t11 isoform g8372.t11 30059490 30060580
chr_2 g8372 g8372.t11 exon g8372.t11.exon1 30059490 30059709
chr_2 g8372 g8372.t11 exon g8372.t11.exon2 30059773 30059986
chr_2 g8372 g8372.t11 cds g8372.t11.CDS1 30059893 30059986
chr_2 g8372 g8372.t11 exon g8372.t11.exon3 30060042 30060099
chr_2 g8372 g8372.t11 cds g8372.t11.CDS2 30060042 30060099
chr_2 g8372 g8372.t11 exon g8372.t11.exon4 30060157 30060361
chr_2 g8372 g8372.t11 cds g8372.t11.CDS3 30060157 30060361
chr_2 g8372 g8372.t11 exon g8372.t11.exon5 30060428 30060580
chr_2 g8372 g8372.t11 cds g8372.t11.CDS4 30060428 30060580
chr_2 g8372 g8372.t11 TSS g8372.t11 30060616 30060616

Sequences

>g8372.t11 Gene=g8372 Length=850
ATGTTAAGAAATATAGTAAAAACGTTGTTAAAAGTTCCAAATACTCGACAATTTGTAACT
GCACCAACTTCATCCATTATTACACAATCAAAAGATCGACTGGCAGAACAAATAAATCAA
TATAATTCGAAATTTTTACCGGAACCAAGAGAAGTTTGGATTGAAAATTTAGATACAGAA
GAAACAAATCGACTCGGTTTGATGAAACTTCATCCTGAAGTTTTTGCTGACACTCCTCGT
ATTGATATTGTACAGAGAAATGTGCAATGGCAAAAGATGTATCGATTTGTGAGTTTTGCT
CATTCAAAAACAAGAGCTGAGAAACGTGGAGGAGGAAGAAAGCCGTGGCCGCAGAAAGGT
CTTGGTAGAGCTCGTCATGGTTCAATAAGATCACCCATCTTTCGTGGTGGTGGTAAGACG
TTGTCATGGTCCACGATCACCCACTCCTCATTTTTACATGCTTCCATTTTGGTTGAGATT
GAAAGGTTTGACCACTACTCTTTCTATTAAACTTGCACAAGATGATCTGCATGTTGTAAA
AGACCTCGAAATTCCAACTAATGATAAAGAATACATTAAAAGCCTTGTTGAGAAAAGAAA
TTGGGGTCCTTCTGTATTGATTGTTGATGATAATGATATCATGCCGAAAAATATTACAAT
AGCAACAGATGAAATAAGTTACATTAATCTTATGCCTGTTTATGGTTTGAATGTTTATTC
AATGTTGAAATATAACACATTAGTGCTAACAAAAGCTGCAGCTGAAAAGATTCAAGAGAA
AATTTTGTTTAATTTGAGACGAACTGATGCATATAAAATGGAAGCTAAGTTCAAAGTCAA
TCAAAATTAA

>g8372.t11 Gene=g8372 Length=169
MLRNIVKTLLKVPNTRQFVTAPTSSIITQSKDRLAEQINQYNSKFLPEPREVWIENLDTE
ETNRLGLMKLHPEVFADTPRIDIVQRNVQWQKMYRFVSFAHSKTRAEKRGGGRKPWPQKG
LGRARHGSIRSPIFRGGGKTLSWSTITHSSFLHASILVEIERFDHYSFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8372.t11 Gene3D G3DSA:3.40.1370.10 - 32 143 0
2 g8372.t11 PANTHER PTHR10746:SF6 39S RIBOSOMAL PROTEIN L4, MITOCHONDRIAL 35 140 0
3 g8372.t11 PANTHER PTHR10746 50S RIBOSOMAL PROTEIN L4 35 140 0
1 g8372.t11 Pfam PF00573 Ribosomal protein L4/L1 family 69 141 0
4 g8372.t11 SUPERFAMILY SSF52166 Ribosomal protein L4 59 141 0

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