General information for g1499.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peptidoglycan-recognition protein LB.
Parent gene
- The parent gene g1499 is located on chr_3: 11407710..11409103 (+ 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_3 | g1499 | g1499.t2 | isoform | g1499.t2 | 11407710 | 11409103 |
| chr_3 | g1499 | g1499.t2 | exon | g1499.t2.exon1 | 11407710 | 11407735 |
| chr_3 | g1499 | g1499.t2 | exon | g1499.t2.exon2 | 11408498 | 11408812 |
| chr_3 | g1499 | g1499.t2 | cds | g1499.t2.CDS1 | 11408635 | 11408812 |
| chr_3 | g1499 | g1499.t2 | exon | g1499.t2.exon3 | 11408886 | 11409103 |
| chr_3 | g1499 | g1499.t2 | cds | g1499.t2.CDS2 | 11408886 | 11409103 |
| chr_3 | g1499 | g1499.t2 | TTS | g1499.t2 | 11409148 | 11409148 |
| chr_3 | g1499 | g1499.t2 | TSS | g1499.t2 | NA | NA |
Sequences
>g1499.t2 Gene=g1499 Length=559
TTTTTACAAATATTTAAATAAAAAATGTTTTGTTGGACGCAATGAATGGGGAGCACGAGA
TCCAAAGTTGGTTGAAAAATTTTCAGGTCAAATACCATTTGTCATTATTCATCACTCATA
TCGACCCGCTGTTTCATTCGACTCAGCTGAATGTGGAAAAGCAATGCGTATAATGCAGGA
CATGCATCAGTTGACAAATGATTGGAATGATATTGGATACAGCTTTGCTATTTGTGGTGA
CGGAAAAATTTATCAGGGTCGTGGCTACAATGTAATAGGAGCACATGCACCACGTTACAA
TGACAAAAGCATTGGAATTTGTCTAATTGGCGATTGGCGATTTGAACTTCCACCAGAACA
AATGCTAAAGGCAACAAAAGATCTCATTGCTTATAGCTTAGAGAATGGCTATTTATCACC
AAATTACAAGGTACTTGGACATCGACAAGTTCGCGCAACTGAATGTCCTGGACAGCGATT
GTATGAAGAGATTGCAACATGGGATCATTATTCAAAGACACCGAGCGGTCCAAGCGACAC
AAATATACCACCGTATTAA
>g1499.t2 Gene=g1499 Length=131
MRIMQDMHQLTNDWNDIGYSFAICGDGKIYQGRGYNVIGAHAPRYNDKSIGICLIGDWRF
ELPPEQMLKATKDLIAYSLENGYLSPNYKVLGHRQVRATECPGQRLYEEIATWDHYSKTP
SGPSDTNIPPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1499.t2 | CDD | cd06583 | PGRP | 1 | 105 | 0e+00 |
| 7 | g1499.t2 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 1 | 122 | 0e+00 |
| 2 | g1499.t2 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 1 | 118 | 0e+00 |
| 3 | g1499.t2 | PANTHER | PTHR11022:SF67 | PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED | 1 | 118 | 0e+00 |
| 1 | g1499.t2 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 12 | 103 | 0e+00 |
| 5 | g1499.t2 | SMART | SM00701 | pgrp | 1 | 97 | 0e+00 |
| 6 | g1499.t2 | SMART | SM00644 | ami_2 | 1 | 103 | 2e-06 |
| 4 | g1499.t2 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 1 | 118 | 0e+00 |
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
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