Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t10 TTS g8372.t10 30059447 30059447
chr_2 g8372 g8372.t10 isoform g8372.t10 30059490 30060580
chr_2 g8372 g8372.t10 exon g8372.t10.exon1 30059490 30059709
chr_2 g8372 g8372.t10 cds g8372.t10.CDS1 30059490 30059709
chr_2 g8372 g8372.t10 exon g8372.t10.exon2 30059773 30059986
chr_2 g8372 g8372.t10 cds g8372.t10.CDS2 30059773 30059986
chr_2 g8372 g8372.t10 exon g8372.t10.exon3 30060046 30060099
chr_2 g8372 g8372.t10 cds g8372.t10.CDS3 30060046 30060099
chr_2 g8372 g8372.t10 exon g8372.t10.exon4 30060157 30060580
chr_2 g8372 g8372.t10 cds g8372.t10.CDS4 30060157 30060313
chr_2 g8372 g8372.t10 TSS g8372.t10 30060616 30060616

Sequences

>g8372.t10 Gene=g8372 Length=912
ATGTTAAGAAATATAGTAAAAACGTTGTTAAAAGTTCCAAATACTCGACAATTTGTAACT
GCACCAACTTCATCCATTATTACACAATCAAAAGATCGACTGGCAGAACAAATAAATCAA
TATAATTCGAAATTTTTACCGGAACCAAGAGAAGTATGGATTTTAAAAGATTATATTAAT
AATCTAGCCAAAGAACTATAAAACATTTAAAACTTGTAGGTTTGGATTGAAAATTTAGAT
ACAGAAGAAACAAATCGACTCGGTTTGATGAAACTTCATCCTGAAGTTTTTGCTGACACT
CCTCGTATTGATATTGTACAGAGAAATGTGCAATGGCAAAAGATGTATCGATTTGTGAGT
TTTGCTCATTCAAAAACAAGAGCTGAGAAACGTGGAGGAGGAAGAAAGCCGTGGCCGCAG
AAAGGTCTTGGTAGAGCTCGTCATGGTTCAATAAGATCACCCATCTTTCGTGGTGGTGGA
CGTTGTCATGGTCCACGATCACCCACTCCTCATTTTTACATGCTTCCATTTTGGTTGAGA
TTGAAAGGTTTGACCACTACTCTTTCTATTAAACTTGCACAAGATGATCTGCATGTTGTA
AAAGACCTCGAAATTCCAACTAATGATAAAGAATACATTAAAAGCCTTGTTGAGAAAAGA
AATTGGGGTCCTTCTGTATTGATTGTTGATGATAATGATATCATGCCGAAAAATATTACA
ATAGCAACAGATGAAATAAGTTACATTAATCTTATGCCTGTTTATGGTTTGAATGTTTAT
TCAATGTTGAAATATAACACATTAGTGCTAACAAAAGCTGCAGCTGAAAAGATTCAAGAG
AAAATTTTGTTTAATTTGAGACGAACTGATGCATATAAAATGGAAGCTAAGTTCAAAGTC
AATCAAAATTAA

>g8372.t10 Gene=g8372 Length=214
MKLHPEVFADTPRIDIVQRNVQWQKMYRFVSFAHSKTRAEKRGGGRKPWPQKGLGRARHG
SIRSPIFRGGGRCHGPRSPTPHFYMLPFWLRLKGLTTTLSIKLAQDDLHVVKDLEIPTND
KEYIKSLVEKRNWGPSVLIVDDNDIMPKNITIATDEISYINLMPVYGLNVYSMLKYNTLV
LTKAAAEKIQEKILFNLRRTDAYKMEAKFKVNQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8372.t10 Gene3D G3DSA:3.40.1370.10 - 1 213 0
2 g8372.t10 PANTHER PTHR10746:SF6 39S RIBOSOMAL PROTEIN L4, MITOCHONDRIAL 1 201 0
3 g8372.t10 PANTHER PTHR10746 50S RIBOSOMAL PROTEIN L4 1 201 0
1 g8372.t10 Pfam PF00573 Ribosomal protein L4/L1 family 2 192 0
4 g8372.t10 SUPERFAMILY SSF52166 Ribosomal protein L4 2 193 0
6 g8372.t10 TIGRFAM TIGR03953 rplD_bact: 50S ribosomal protein uL4 2 191 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

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. There were no conditions that were differentially expressed