General information for g10465.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peptidoglycan-recognition protein LF.
Parent gene
- The parent gene g10465 is located on chr_1: 9978080..9979320 (+ 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_1 | g10465 | g10465.t4 | isoform | g10465.t4 | 9976896 | 9979320 |
| chr_1 | g10465 | g10465.t4 | exon | g10465.t4.exon1 | 9976896 | 9977055 |
| chr_1 | g10465 | g10465.t4 | TSS | g10465.t4 | 9976897 | 9976897 |
| chr_1 | g10465 | g10465.t4 | exon | g10465.t4.exon2 | 9978471 | 9978595 |
| chr_1 | g10465 | g10465.t4 | cds | g10465.t4.CDS1 | 9978575 | 9978595 |
| chr_1 | g10465 | g10465.t4 | exon | g10465.t4.exon3 | 9978798 | 9978906 |
| chr_1 | g10465 | g10465.t4 | cds | g10465.t4.CDS2 | 9978798 | 9978906 |
| chr_1 | g10465 | g10465.t4 | exon | g10465.t4.exon4 | 9978965 | 9979000 |
| chr_1 | g10465 | g10465.t4 | cds | g10465.t4.CDS3 | 9978965 | 9979000 |
| chr_1 | g10465 | g10465.t4 | exon | g10465.t4.exon5 | 9979064 | 9979320 |
| chr_1 | g10465 | g10465.t4 | cds | g10465.t4.CDS4 | 9979064 | 9979320 |
| chr_1 | g10465 | g10465.t4 | TTS | g10465.t4 | 9979390 | 9979390 |
Sequences
>g10465.t4 Gene=g10465 Length=687
ATCAGTTTCATACAGTGAGTCATTTGTATCACTTCATTTTATTTTTTAATCAAGAAAGCG
AAAAAACTTTTTTTTTTTAAAAAAATGTCCATGTCATTAGAAATTCAAAGTAAGAAAATC
GCTGAGAATAACAATAAAAAGTCCTTAAATTGCTATTGCTAAATTTATAGATTTTATACT
AGAGAAGATTGGAATGCAAGTAAAGCTGAGCCTTATTTTAAATTAATTCATCCTATTAAG
AGAGTTATTATTTCTCATACAGTCATGAGAGAATGTTATGTTGAGAAAGAATGCATATGG
ATTGTGCAAGAAATACAAAGACTTCATAAAAATTGGGATTTTGGTGATATTGGATTTAAT
TTTGTCATCATGAATGATGGAAGCATTTTTGAAGGAAGAGGTTGGGACATTATGGGTGCT
CATACACGAGGCTTTAATAATAACAGTATAGGTATCGTATACAATGGCAATTTTCAAACT
CAAAGTCCACCACAAAAGCAAATTCTTGCGGGATTTTCTTTACTTGAAGAAGGAGTTCGT
TTAGGAAAATTATCACCAGATTTTAAAATCTATGGAATGCGACAATTTCAAAGTAATGAA
AGTCCTGGTGAAGCTTTCTTTCAAATGATTAAAACATGGAAAAATTGGTCTGAAGATATT
GATGAATGTTGTCCAAAACCAACATAA
>g10465.t4 Gene=g10465 Length=140
MRECYVEKECIWIVQEIQRLHKNWDFGDIGFNFVIMNDGSIFEGRGWDIMGAHTRGFNNN
SIGIVYNGNFQTQSPPQKQILAGFSLLEEGVRLGKLSPDFKIYGMRQFQSNESPGEAFFQ
MIKTWKNWSEDIDECCPKPT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10465.t4 | CDD | cd06583 | PGRP | 13 | 117 | 0 |
| 5 | g10465.t4 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 1 | 135 | 0 |
| 2 | g10465.t4 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 3 | 128 | 0 |
| 1 | g10465.t4 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 24 | 115 | 0 |
| 4 | g10465.t4 | SMART | SM00701 | pgrp | 1 | 109 | 0 |
| 3 | g10465.t4 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 3 | 130 | 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