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.t7 isoform g11401.t7 15970527 15971614
chr_1 g11401 g11401.t7 exon g11401.t7.exon1 15970527 15970550
chr_1 g11401 g11401.t7 cds g11401.t7.CDS1 15970527 15970550
chr_1 g11401 g11401.t7 exon g11401.t7.exon2 15970764 15970894
chr_1 g11401 g11401.t7 cds g11401.t7.CDS2 15970764 15970894
chr_1 g11401 g11401.t7 exon g11401.t7.exon3 15971104 15971358
chr_1 g11401 g11401.t7 cds g11401.t7.CDS3 15971104 15971358
chr_1 g11401 g11401.t7 exon g11401.t7.exon4 15971478 15971614
chr_1 g11401 g11401.t7 cds g11401.t7.CDS4 15971478 15971577
chr_1 g11401 g11401.t7 TTS g11401.t7 15971690 15971690
chr_1 g11401 g11401.t7 TSS g11401.t7 NA NA

Sequences

>g11401.t7 Gene=g11401 Length=547
ATGTCTTACAAGTTTTCAAATAAGGCAATTGTCATTGATGGTCGTGGCCATCTCTTGGGA
CGATTGGCATCAATTGTCGCAAAGCAAATTTTAAACGGTACCAAGGTTGTTATCGTAAGA
TGCGAAGATTTACAACTTTCAGGTCATTTCTTCAGAAACAAAATTAAGTTCTTGTCGTTC
CTTCGCAAGCGCTGTAATGTCAACCCAGCTCGTGGTCCATTCCATTTCCGCGCACCAAGT
CGTATGTTTTGGAAAGCTGTTCGCGGAATGGTTCCACATAAAACACGCCGTGGAAAGCTT
GCATTAGCTCGTTTAAAGGTCTTTGAAGGAATTCCACCACCATATGACAAGCAAAAGCGA
GTTTGTGTTCCTCTTGCTATGAAAATTTTGTGCTTACGATCAGACAGAAATGGAAAAACT
TCGTCTACGTGCTACACAAAAAGTTTCAAAAGGAATCGCCAAACAAAATTCCATTCTCAA
AAAGTTCGGATATATCACATCAGAAAATGAAGTGAAGCCAGTCGCCGCCGTCGCAGCAAA
GGCATAA

>g11401.t7 Gene=g11401 Length=169
MSYKFSNKAIVIDGRGHLLGRLASIVAKQILNGTKVVIVRCEDLQLSGHFFRNKIKFLSF
LRKRCNVNPARGPFHFRAPSRMFWKAVRGMVPHKTRRGKLALARLKVFEGIPPPYDKQKR
VCVPLAMKILCLRSDRNGKTSSTCYTKSFKRNRQTKFHSQKVRIYHIRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11401.t7 CDD cd00392 Ribosomal_L13 10 111 4.90594E-40
6 g11401.t7 Gene3D G3DSA:3.90.1180.10 - 5 148 3.6E-59
4 g11401.t7 Hamap MF_01366 50S ribosomal protein L13 [rplM]. 9 126 18.735836
2 g11401.t7 PANTHER PTHR11545:SF3 60S RIBOSOMAL PROTEIN L13A-RELATED 4 136 8.7E-63
3 g11401.t7 PANTHER PTHR11545 RIBOSOMAL PROTEIN L13 4 136 8.7E-63
7 g11401.t7 PIRSF PIRSF002181 RPL13p_RPL13Aa_RPL16e_RPL13o 1 163 7.3E-39
1 g11401.t7 Pfam PF00572 Ribosomal protein L13 8 113 2.5E-24
9 g11401.t7 ProSitePatterns PS00783 Ribosomal protein L13 signature. 87 110 -
5 g11401.t7 SUPERFAMILY SSF52161 Ribosomal protein L13 10 129 6.41E-45
10 g11401.t7 TIGRFAM TIGR01077 L13_A_E: ribosomal protein uL13 10 127 3.4E-48

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