General information for g11401.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L13a.
Parent gene
- The parent gene g11401 is located on chr_1: 15971204..15980307 (+ 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 | g11401 | g11401.t10 | isoform | g11401.t10 | 15970527 | 15971692 |
| chr_1 | g11401 | g11401.t10 | exon | g11401.t10.exon1 | 15970527 | 15970550 |
| chr_1 | g11401 | g11401.t10 | cds | g11401.t10.CDS1 | 15970527 | 15970550 |
| chr_1 | g11401 | g11401.t10 | exon | g11401.t10.exon2 | 15970764 | 15970894 |
| chr_1 | g11401 | g11401.t10 | cds | g11401.t10.CDS2 | 15970764 | 15970894 |
| chr_1 | g11401 | g11401.t10 | exon | g11401.t10.exon3 | 15971104 | 15971312 |
| chr_1 | g11401 | g11401.t10 | cds | g11401.t10.CDS3 | 15971104 | 15971312 |
| chr_1 | g11401 | g11401.t10 | exon | g11401.t10.exon4 | 15971447 | 15971692 |
| chr_1 | g11401 | g11401.t10 | cds | g11401.t10.CDS4 | 15971447 | 15971469 |
| chr_1 | g11401 | g11401.t10 | TTS | g11401.t10 | 15971690 | 15971690 |
| chr_1 | g11401 | g11401.t10 | TSS | g11401.t10 | NA | NA |
Sequences
>g11401.t10 Gene=g11401 Length=610
ATGTCTTACAAGTTTTCAAATAAGGCAATTGTCATTGATGGTCGTGGCCATCTCTTGGGA
CGATTGGCATCAATTGTCGCAAAGCAAATTTTAAACGGTACCAAGGTTGTTATCGTAAGA
TGCGAAGATTTACAACTTTCAGGTCATTTCTTCAGAAACAAAATTAAGTTCTTGTCGTTC
CTTCGCAAGCGCTGTAATGTCAACCCAGCTCGTGGTCCATTCCATTTCCGCGCACCAAGT
CGTATGTTTTGGAAAGCTGTTCGCGGAATGGTTCCACATAAAACACGCCGTGGAAAGCTT
GCATTAGCTCGTTTAAAGGTCTTTGAAGGAATTCCACCACCATATGACAAGCAAAAGCGA
GTTTGCACGCTTGTATTACAACCATAAACAACGTTTGGAAAAACTTCGTCTACGTGCTAC
ACAAAAAGTTTCAAAAGGAATCGCCAAACAAAATTCCATTCTCAAAAAGTTCGGATATAT
CACATCAGAAAATGAAGTGAAGCCAGTCGCCGCCGTCGCAGCAAAGGCATAAACTTTTGA
CCGAAAACATGAAATAAAGAAGTTAAAAAGGATTCAATAAAATCAATGAACCTATTCTGA
AATAATTTAA
>g11401.t10 Gene=g11401 Length=128
MSYKFSNKAIVIDGRGHLLGRLASIVAKQILNGTKVVIVRCEDLQLSGHFFRNKIKFLSF
LRKRCNVNPARGPFHFRAPSRMFWKAVRGMVPHKTRRGKLALARLKVFEGIPPPYDKQKR
VCTLVLQP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11401.t10 | CDD | cd00392 | Ribosomal_L13 | 10 | 111 | 2.05056E-41 |
| 6 | g11401.t10 | Gene3D | G3DSA:3.90.1180.10 | - | 5 | 127 | 8.8E-56 |
| 4 | g11401.t10 | Hamap | MF_01366 | 50S ribosomal protein L13 [rplM]. | 9 | 127 | 18.691706 |
| 2 | g11401.t10 | PANTHER | PTHR11545:SF3 | 60S RIBOSOMAL PROTEIN L13A-RELATED | 4 | 122 | 7.3E-59 |
| 3 | g11401.t10 | PANTHER | PTHR11545 | RIBOSOMAL PROTEIN L13 | 4 | 122 | 7.3E-59 |
| 7 | g11401.t10 | PIRSF | PIRSF002181 | RPL13p_RPL13Aa_RPL16e_RPL13o | 1 | 127 | 4.1E-37 |
| 1 | g11401.t10 | Pfam | PF00572 | Ribosomal protein L13 | 8 | 113 | 1.0E-24 |
| 9 | g11401.t10 | ProSitePatterns | PS00783 | Ribosomal protein L13 signature. | 87 | 110 | - |
| 5 | g11401.t10 | SUPERFAMILY | SSF52161 | Ribosomal protein L13 | 10 | 122 | 1.1E-43 |
| 10 | g11401.t10 | TIGRFAM | TIGR01077 | L13_A_E: ribosomal protein uL13 | 10 | 121 | 2.7E-47 |
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:0015934 | large ribosomal subunit | 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