Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L13a.

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_1 g11401 g11401.t14 isoform g11401.t14 15970527 15972286
chr_1 g11401 g11401.t14 exon g11401.t14.exon1 15970527 15970550
chr_1 g11401 g11401.t14 cds g11401.t14.CDS1 15970527 15970550
chr_1 g11401 g11401.t14 exon g11401.t14.exon2 15970764 15970894
chr_1 g11401 g11401.t14 cds g11401.t14.CDS2 15970764 15970894
chr_1 g11401 g11401.t14 exon g11401.t14.exon3 15971104 15971634
chr_1 g11401 g11401.t14 cds g11401.t14.CDS3 15971104 15971614
chr_1 g11401 g11401.t14 exon g11401.t14.exon4 15972143 15972286
chr_1 g11401 g11401.t14 TSS g11401.t14 NA NA
chr_1 g11401 g11401.t14 TTS g11401.t14 NA NA

Sequences

>g11401.t14 Gene=g11401 Length=830
ATGTCTTACAAGTTTTCAAATAAGGCAATTGTCATTGATGGTCGTGGCCATCTCTTGGGA
CGATTGGCATCAATTGTCGCAAAGCAAATTTTAAACGGTACCAAGGTTGTTATCGTAAGA
TGCGAAGATTTACAACTTTCAGGTCATTTCTTCAGAAACAAAATTAAGTTCTTGTCGTTC
CTTCGCAAGCGCTGTAATGTCAACCCAGCTCGTGGTCCATTCCATTTCCGCGCACCAAGT
CGTATGTTTTGGAAAGCTGTTCGCGGAATGGTTCCACATAAAACACGCCGTGGAAAGCTT
GCATTAGCTCGTTTAAAGGTCTTTGAAGGAATTCCACCACCATATGACAAGCAAAAGCGA
GTTTGTGTTCCTCTTGCTATGAAAATTTTGTGCTTACGATCAGACAGAAAGTATTGCCAA
GTAGGACGTGTAGCTCATGAAGTTGGTTGGCAATATAAAGATGTTGTAAGCAGTCTTGAA
GCAAAGAGAAAGATCAAGGCACGCTTGTATTACAACCATAAACAACGTTTGGAAAAACTT
CGTCTACGTGCTACACAAAAAGTTTCAAAAGGAATCGCCAAACAAAATTCCATTCTCAAA
AAGTTCGGATATATCACATCAGAAAATGAAGTGAAGCCAGTCGCCGCCGTCGCAGCAAAG
GCATAAACTTTTGACCGAAAACATGAATAAAAAAGTTAAAAAAATTTAATGCAGTCTCTA
TGCACTTAATTACAGGAGAGTTTTTATGACATAGCTATATCTTAAATTTTATGCAAACTG
TCTTTATTTAAAAAAATAAATAAAATGTGTTAATTACATTAAGAACAATT

>g11401.t14 Gene=g11401 Length=221
MSYKFSNKAIVIDGRGHLLGRLASIVAKQILNGTKVVIVRCEDLQLSGHFFRNKIKFLSF
LRKRCNVNPARGPFHFRAPSRMFWKAVRGMVPHKTRRGKLALARLKVFEGIPPPYDKQKR
VCVPLAMKILCLRSDRKYCQVGRVAHEVGWQYKDVVSSLEAKRKIKARLYYNHKQRLEKL
RLRATQKVSKGIAKQNSILKKFGYITSENEVKPVAAVAAKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11401.t14 CDD cd00392 Ribosomal_L13 10 111 2.14685E-39
6 g11401.t14 Gene3D G3DSA:3.90.1180.10 - 5 152 6.8E-68
4 g11401.t14 Hamap MF_01366 50S ribosomal protein L13 [rplM]. 9 126 18.735836
2 g11401.t14 PANTHER PTHR11545:SF3 60S RIBOSOMAL PROTEIN L13A-RELATED 4 204 7.1E-90
3 g11401.t14 PANTHER PTHR11545 RIBOSOMAL PROTEIN L13 4 204 7.1E-90
1 g11401.t14 Pfam PF00572 Ribosomal protein L13 8 113 5.1E-24
8 g11401.t14 ProSitePatterns PS00783 Ribosomal protein L13 signature. 87 110 -
5 g11401.t14 SUPERFAMILY SSF52161 Ribosomal protein L13 10 152 1.3E-49
9 g11401.t14 TIGRFAM TIGR01077 L13_A_E: ribosomal protein uL13 10 152 3.3E-54

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

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.

Raw TPM values