General information for g11209.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L35.
Parent gene
- The parent gene g11209 is located on chr_1: 14596344..14596964 (+ 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_1 | g11209 | g11209.t1 | isoform | g11209.t1 | 14596344 | 14596964 |
| chr_1 | g11209 | g11209.t1 | exon | g11209.t1.exon1 | 14596344 | 14596346 |
| chr_1 | g11209 | g11209.t1 | cds | g11209.t1.CDS1 | 14596344 | 14596346 |
| chr_1 | g11209 | g11209.t1 | exon | g11209.t1.exon2 | 14596535 | 14596671 |
| chr_1 | g11209 | g11209.t1 | cds | g11209.t1.CDS2 | 14596535 | 14596671 |
| chr_1 | g11209 | g11209.t1 | exon | g11209.t1.exon3 | 14596733 | 14596964 |
| chr_1 | g11209 | g11209.t1 | cds | g11209.t1.CDS3 | 14596733 | 14596964 |
| chr_1 | g11209 | g11209.t1 | TTS | g11209.t1 | 14597030 | 14597030 |
| chr_1 | g11209 | g11209.t1 | TSS | g11209.t1 | NA | NA |
Sequences
>g11209.t1 Gene=g11209 Length=372
ATGGGCAAAGTGAAGTGTTCAGAATTGAGACAAAAGGACAAGAAGGAGTTGACAAAACAA
CTCGAAGACCTTAAGCAAGAGCTTCTCGGACTTCGTGTTGCCAAAGTCACAGGAGGTGCA
CCTTCAAAACTTTCAAAGATCCGTGTTGTACGCAAAGCAATTGCTCGCGTATACATTGTT
ATGAACCAGAAGACAAAGGAGAATCTTCGTAAATTGTACAAGGGAAAGAAATACAAGCCA
TTGGACTTGAGACCCAAAAAGACCCGAGCAATGAGACGTGCACTCAGTGAACGCGATGCT
AGCCGATTAACAAAAAAGGAAATTCGTAAGCGTTCAGTATATCCAGTTCGCAAATACGCT
GTTAAGGCATAA
>g11209.t1 Gene=g11209 Length=123
MGKVKCSELRQKDKKELTKQLEDLKQELLGLRVAKVTGGAPSKLSKIRVVRKAIARVYIV
MNQKTKENLRKLYKGKKYKPLDLRPKKTRAMRRALSERDASRLTKKEIRKRSVYPVRKYA
VKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11209.t1 | CDD | cd00427 | Ribosomal_L29_HIP | 7 | 64 | 2.08208E-12 |
| 8 | g11209.t1 | Coils | Coil | Coil | 7 | 34 | - |
| 7 | g11209.t1 | Gene3D | G3DSA:1.10.287.310 | - | 2 | 77 | 2.2E-35 |
| 6 | g11209.t1 | Gene3D | G3DSA:1.10.20.90 | - | 78 | 123 | 5.6E-21 |
| 4 | g11209.t1 | Hamap | MF_00374 | 50S ribosomal protein L29 [rpmC]. | 4 | 64 | 12.842689 |
| 2 | g11209.t1 | PANTHER | PTHR45722:SF9 | 60S RIBOSOMAL PROTEIN L35 | 1 | 123 | 1.8E-45 |
| 3 | g11209.t1 | PANTHER | PTHR45722 | 60S RIBOSOMAL PROTEIN L35 | 1 | 123 | 1.8E-45 |
| 1 | g11209.t1 | Pfam | PF00831 | Ribosomal L29 protein | 7 | 64 | 9.6E-20 |
| 10 | g11209.t1 | ProSitePatterns | PS00579 | Ribosomal protein L29 signature. | 43 | 57 | - |
| 5 | g11209.t1 | SUPERFAMILY | SSF46561 | Ribosomal protein L29 (L29p) | 4 | 64 | 8.9E-18 |
| 11 | g11209.t1 | TIGRFAM | TIGR00012 | L29: ribosomal protein uL29 | 8 | 64 | 6.0E-19 |
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 K02918 (large subunit ribosomal protein L35e)
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.
