General information for g8372.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L4, mitochondrial.
Parent gene
- The parent gene g8372 is located on chr_2: 30059490..30060580 (- strand)
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.t1 | TTS | g8372.t1 | 30059447 | 30059447 |
| chr_2 | g8372 | g8372.t1 | isoform | g8372.t1 | 30059490 | 30060580 |
| chr_2 | g8372 | g8372.t1 | exon | g8372.t1.exon1 | 30059490 | 30059709 |
| chr_2 | g8372 | g8372.t1 | cds | g8372.t1.CDS1 | 30059490 | 30059709 |
| chr_2 | g8372 | g8372.t1 | exon | g8372.t1.exon2 | 30059773 | 30059986 |
| chr_2 | g8372 | g8372.t1 | cds | g8372.t1.CDS2 | 30059773 | 30059986 |
| chr_2 | g8372 | g8372.t1 | exon | g8372.t1.exon3 | 30060046 | 30060099 |
| chr_2 | g8372 | g8372.t1 | cds | g8372.t1.CDS3 | 30060046 | 30060099 |
| chr_2 | g8372 | g8372.t1 | exon | g8372.t1.exon4 | 30060157 | 30060361 |
| chr_2 | g8372 | g8372.t1 | cds | g8372.t1.CDS4 | 30060157 | 30060361 |
| chr_2 | g8372 | g8372.t1 | exon | g8372.t1.exon5 | 30060428 | 30060580 |
| chr_2 | g8372 | g8372.t1 | cds | g8372.t1.CDS5 | 30060428 | 30060580 |
| chr_2 | g8372 | g8372.t1 | TSS | g8372.t1 | 30060616 | 30060616 |
Sequences
>g8372.t1 Gene=g8372 Length=846
ATGTTAAGAAATATAGTAAAAACGTTGTTAAAAGTTCCAAATACTCGACAATTTGTAACT
GCACCAACTTCATCCATTATTACACAATCAAAAGATCGACTGGCAGAACAAATAAATCAA
TATAATTCGAAATTTTTACCGGAACCAAGAGAAGTTTGGATTGAAAATTTAGATACAGAA
GAAACAAATCGACTCGGTTTGATGAAACTTCATCCTGAAGTTTTTGCTGACACTCCTCGT
ATTGATATTGTACAGAGAAATGTGCAATGGCAAAAGATGTATCGATTTGTGAGTTTTGCT
CATTCAAAAACAAGAGCTGAGAAACGTGGAGGAGGAAGAAAGCCGTGGCCGCAGAAAGGT
CTTGGTAGAGCTCGTCATGGTTCAATAAGATCACCCATCTTTCGTGGTGGTGGACGTTGT
CATGGTCCACGATCACCCACTCCTCATTTTTACATGCTTCCATTTTGGTTGAGATTGAAA
GGTTTGACCACTACTCTTTCTATTAAACTTGCACAAGATGATCTGCATGTTGTAAAAGAC
CTCGAAATTCCAACTAATGATAAAGAATACATTAAAAGCCTTGTTGAGAAAAGAAATTGG
GGTCCTTCTGTATTGATTGTTGATGATAATGATATCATGCCGAAAAATATTACAATAGCA
ACAGATGAAATAAGTTACATTAATCTTATGCCTGTTTATGGTTTGAATGTTTATTCAATG
TTGAAATATAACACATTAGTGCTAACAAAAGCTGCAGCTGAAAAGATTCAAGAGAAAATT
TTGTTTAATTTGAGACGAACTGATGCATATAAAATGGAAGCTAAGTTCAAAGTCAATCAA
AATTAA
>g8372.t1 Gene=g8372 Length=281
MLRNIVKTLLKVPNTRQFVTAPTSSIITQSKDRLAEQINQYNSKFLPEPREVWIENLDTE
ETNRLGLMKLHPEVFADTPRIDIVQRNVQWQKMYRFVSFAHSKTRAEKRGGGRKPWPQKG
LGRARHGSIRSPIFRGGGRCHGPRSPTPHFYMLPFWLRLKGLTTTLSIKLAQDDLHVVKD
LEIPTNDKEYIKSLVEKRNWGPSVLIVDDNDIMPKNITIATDEISYINLMPVYGLNVYSM
LKYNTLVLTKAAAEKIQEKILFNLRRTDAYKMEAKFKVNQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g8372.t1 | Gene3D | G3DSA:3.40.1370.10 | - | 34 | 279 | 0 |
| 2 | g8372.t1 | PANTHER | PTHR10746:SF6 | 39S RIBOSOMAL PROTEIN L4, MITOCHONDRIAL | 35 | 267 | 0 |
| 3 | g8372.t1 | PANTHER | PTHR10746 | 50S RIBOSOMAL PROTEIN L4 | 35 | 267 | 0 |
| 1 | g8372.t1 | Pfam | PF00573 | Ribosomal protein L4/L1 family | 69 | 259 | 0 |
| 4 | g8372.t1 | SUPERFAMILY | SSF52166 | Ribosomal protein L4 | 60 | 260 | 0 |
| 6 | g8372.t1 | TIGRFAM | TIGR03953 | rplD_bact: 50S ribosomal protein uL4 | 69 | 258 | 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 transcript has been annotated with K02926 (large subunit ribosomal protein L4)
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.
