General information for g6527.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peptidoglycan-recognition protein SC2.
Parent gene
- The parent gene g6527 is located on chr_2: 17485079..17487903 (- 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_2 | g6527 | g6527.t1 | isoform | g6527.t1 | 17485079 | 17485688 |
| chr_2 | g6527 | g6527.t1 | exon | g6527.t1.exon1 | 17485079 | 17485368 |
| chr_2 | g6527 | g6527.t1 | cds | g6527.t1.CDS1 | 17485079 | 17485368 |
| chr_2 | g6527 | g6527.t1 | exon | g6527.t1.exon2 | 17485422 | 17485436 |
| chr_2 | g6527 | g6527.t1 | cds | g6527.t1.CDS2 | 17485422 | 17485436 |
| chr_2 | g6527 | g6527.t1 | exon | g6527.t1.exon3 | 17485504 | 17485585 |
| chr_2 | g6527 | g6527.t1 | cds | g6527.t1.CDS3 | 17485504 | 17485585 |
| chr_2 | g6527 | g6527.t1 | exon | g6527.t1.exon4 | 17485644 | 17485688 |
| chr_2 | g6527 | g6527.t1 | cds | g6527.t1.CDS4 | 17485644 | 17485688 |
| chr_2 | g6527 | g6527.t1 | TSS | g6527.t1 | NA | NA |
| chr_2 | g6527 | g6527.t1 | TTS | g6527.t1 | NA | NA |
Sequences
>g6527.t1 Gene=g6527 Length=432
ATGGCATTGCTTTCACATACAGTGACTGGAACTTGTAACAATTATTCTACTTGTGCAACA
TTGATAAGAAATATCCAAAGAGGAAATATAAACAATCAAGGTTTTATTGATCTTGCTTAT
AATTTTGGTATCGGTGGTGATGGGTCGATTTTTGAAGCACGTGGTTTCGACAACGTCGGT
GCACATATGGCCAATTTCAATTCAAAATCAATTGGAATAGGAGCAATGGGACAATTTGAT
ATTGATGAGCCGACTCTTGAAATGCTTGATGCACTTGAAAAATTTCTAGAAGATGCTGCA
AAATTAGGAAAATTACCTGAAGATTACAAAGTACATGGAAGACAAGATTTTGGTTATAAT
GGTCCAGGAGAAAATATTATGAAACATATCCGAGAATGGTGTCGATATGGAAATAGGACA
ATACCATGTTAA
>g6527.t1 Gene=g6527 Length=143
MALLSHTVTGTCNNYSTCATLIRNIQRGNINNQGFIDLAYNFGIGGDGSIFEARGFDNVG
AHMANFNSKSIGIGAMGQFDIDEPTLEMLDALEKFLEDAAKLGKLPEDYKVHGRQDFGYN
GPGENIMKHIREWCRYGNRTIPC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6527.t1 | CDD | cd06583 | PGRP | 4 | 117 | 0 |
| 5 | g6527.t1 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 1 | 140 | 0 |
| 2 | g6527.t1 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 5 | 136 | 0 |
| 1 | g6527.t1 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 5 | 115 | 0 |
| 4 | g6527.t1 | SMART | SM00701 | pgrp | 1 | 118 | 0 |
| 3 | g6527.t1 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 3 | 136 | 0 |
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