Gene loci information

Transcript annotation

  • This transcript has been annotated as Peptidoglycan-recognition protein LB.

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_3 g1499 g1499.t1 TSS g1499.t1 11405800 11405800
chr_3 g1499 g1499.t1 isoform g1499.t1 11405923 11409103
chr_3 g1499 g1499.t1 exon g1499.t1.exon1 11405923 11406028
chr_3 g1499 g1499.t1 cds g1499.t1.CDS1 11405923 11406028
chr_3 g1499 g1499.t1 exon g1499.t1.exon2 11408498 11408812
chr_3 g1499 g1499.t1 cds g1499.t1.CDS2 11408498 11408812
chr_3 g1499 g1499.t1 exon g1499.t1.exon3 11408886 11409103
chr_3 g1499 g1499.t1 cds g1499.t1.CDS3 11408886 11409103
chr_3 g1499 g1499.t1 TTS g1499.t1 11409148 11409148

Sequences

>g1499.t1 Gene=g1499 Length=639
ATGAAGTGGACTTTTGTGCTCAGTATGTACTTGACAATTCTTATTAGCTCAAAAGTAGGT
GAAATTAATAGCTGCCGCATGTTGAATGCAATAAATACAAACATTAGTTTTGTTGGACGC
AATGAATGGGGAGCACGAGATCCAAAGTTGGTTGAAAAATTTTCAGGTCAAATACCATTT
GTCATTATTCATCACTCATATCGACCCGCTGTTTCATTCGACTCAGCTGAATGTGGAAAA
GCAATGCGTATAATGCAGGACATGCATCAGTTGACAAATGATTGGAATGATATTGGATAC
AGCTTTGCTATTTGTGGTGACGGAAAAATTTATCAGGGTCGTGGCTACAATGTAATAGGA
GCACATGCACCACGTTACAATGACAAAAGCATTGGAATTTGTCTAATTGGCGATTGGCGA
TTTGAACTTCCACCAGAACAAATGCTAAAGGCAACAAAAGATCTCATTGCTTATAGCTTA
GAGAATGGCTATTTATCACCAAATTACAAGGTACTTGGACATCGACAAGTTCGCGCAACT
GAATGTCCTGGACAGCGATTGTATGAAGAGATTGCAACATGGGATCATTATTCAAAGACA
CCGAGCGGTCCAAGCGACACAAATATACCACCGTATTAA

>g1499.t1 Gene=g1499 Length=212
MKWTFVLSMYLTILISSKVGEINSCRMLNAINTNISFVGRNEWGARDPKLVEKFSGQIPF
VIIHHSYRPAVSFDSAECGKAMRIMQDMHQLTNDWNDIGYSFAICGDGKIYQGRGYNVIG
AHAPRYNDKSIGICLIGDWRFELPPEQMLKATKDLIAYSLENGYLSPNYKVLGHRQVRAT
ECPGQRLYEEIATWDHYSKTPSGPSDTNIPPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1499.t1 CDD cd06583 PGRP 58 186 3.6827E-45
6 g1499.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 27 203 4.8E-59
2 g1499.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 32 199 1.7E-70
3 g1499.t1 PANTHER PTHR11022:SF67 PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED 32 199 1.7E-70
12 g1499.t1 PIRSF PIRSF037945 PGRP-S 1 202 8.5E-77
1 g1499.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 57 184 5.8E-21
8 g1499.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
9 g1499.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
10 g1499.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
11 g1499.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
7 g1499.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 212 -
14 g1499.t1 SMART SM00701 pgrp 35 178 7.8E-59
15 g1499.t1 SMART SM00644 ami_2 45 184 1.3E-23
4 g1499.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 36 199 6.67E-62
5 g1499.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 24 -

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:0008745 N-acetylmuramoyl-L-alanine amidase activity MF
GO:0008270 zinc ion binding MF
GO:0042834 peptidoglycan binding MF
GO:0045087 innate immune response BP
GO:0009253 peptidoglycan catabolic process BP

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. There were no conditions that were differentially expressed