Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peptidoglycan-recognition protein 1.

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 g9461 g9461.t3 TTS g9461.t3 3191267 3191267
chr_1 g9461 g9461.t3 isoform g9461.t3 3191419 3192044
chr_1 g9461 g9461.t3 exon g9461.t3.exon1 3191419 3191702
chr_1 g9461 g9461.t3 cds g9461.t3.CDS1 3191419 3191702
chr_1 g9461 g9461.t3 exon g9461.t3.exon2 3191768 3192044
chr_1 g9461 g9461.t3 cds g9461.t3.CDS2 3191768 3192044
chr_1 g9461 g9461.t3 TSS g9461.t3 3192067 3192067

Sequences

>g9461.t3 Gene=g9461 Length=561
ATGAAGCTGGCAATTGTGCTTGCTTTTGTGGCCTTTGCATCGGCCCAAAATCCGTGTCAA
AATATTCGTACAAGAACTCAATGGGGCTCACGTTCAACTAGCTTAACATGGATGGCTACA
CGTCCACCAAGTGGTTTCGTCATTCATCATACTGCTGGTGCTCGTTGCACAACTCAAGCA
GCTTGTGACGCAATGATGAGAAATCTTCAAAACTTCCATATGGATACAAACGGTTGGGCT
GATATTGGATACAATTTCTGCATTGGTGATCCAGGTTTTTATGAAGGAAGAGGTTATGGT
CGACATGGAGCTCATTCACCAGGTTTTAGTGCTCGTTCTTTAGGTCATTGTTTCATTGGT
GATCACACAAATGTACTTCCAACAGCTGCCGCTTTAAGTAATACTCAAGCATTCATCACT
TGCTCACGTAATAATGGTGAACTTACTTCTGGACACTGGGTTTCAACACACAGAAACGAT
CAACAAACAGTAACAGCCTGTCCTGGTCAAGCATTGTTCAATGTTGTCTCAACTTGGGAT
CGCTTCCATCCAGTCCCTTAA

>g9461.t3 Gene=g9461 Length=186
MKLAIVLAFVAFASAQNPCQNIRTRTQWGSRSTSLTWMATRPPSGFVIHHTAGARCTTQA
ACDAMMRNLQNFHMDTNGWADIGYNFCIGDPGFYEGRGYGRHGAHSPGFSARSLGHCFIG
DHTNVLPTAAALSNTQAFITCSRNNGELTSGHWVSTHRNDQQTVTACPGQALFNVVSTWD
RFHPVP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9461.t3 CDD cd06583 PGRP 42 171 5.95652E-30
5 g9461.t3 Gene3D G3DSA:3.40.80.10 Lysozyme 11 185 3.1E-48
2 g9461.t3 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 12 182 3.5E-49
1 g9461.t3 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 40 169 1.6E-12
7 g9461.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
8 g9461.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
9 g9461.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 10 -
10 g9461.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 15 -
6 g9461.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 186 -
13 g9461.t3 SMART SM00701 pgrp 20 161 3.9E-33
14 g9461.t3 SMART SM00644 ami_2 33 169 1.6E-9
3 g9461.t3 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 19 184 1.83E-46
4 g9461.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 15 -
12 g9461.t3 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 15 -

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: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