General information for g6528.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peptidoglycan recognition protein 3.
Parent gene
- The parent gene g6528 is located on chr_2: 17488415..17489847 (- 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 | g6528 | g6528.t1 | isoform | g6528.t1 | 17488415 | 17489847 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon1 | 17488415 | 17488704 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS1 | 17488415 | 17488704 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon2 | 17488761 | 17488857 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS2 | 17488761 | 17488857 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon3 | 17488914 | 17489038 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS3 | 17488914 | 17489038 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon4 | 17489099 | 17489194 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS4 | 17489099 | 17489194 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon5 | 17489305 | 17489473 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS5 | 17489305 | 17489473 |
| chr_2 | g6528 | g6528.t1 | exon | g6528.t1.exon6 | 17489539 | 17489847 |
| chr_2 | g6528 | g6528.t1 | cds | g6528.t1.CDS6 | 17489539 | 17489847 |
| chr_2 | g6528 | g6528.t1 | TSS | g6528.t1 | NA | NA |
| chr_2 | g6528 | g6528.t1 | TTS | g6528.t1 | NA | NA |
Sequences
>g6528.t1 Gene=g6528 Length=1086
ATGGATAAAAATAATCTTGTGCACAATAATTCTTTAAATTCTAGAAAATATTTTCAAGGA
ATAAATAGAAAAAGAAACATTTTGATAACGATATTTTCAGTGGCTTTTATTCTCGTAATT
TTAACTACTGTTTCAATTCTTTATTTTGTATTAAAAACTGATTCAAATTCTGATGATTTT
AAATTTGAAAACTTAATTTCAAGAGACGAATGGAATGCTGCACCTCCTAAATCTGGCATT
CCTTTTCTAGAGAGTCCAATTAAAAGAATAATAATTGCACACACTGCAGGAGAATTTTGT
GACAATGAGAATGAATGTAAATTTGTCGTAAAAAGAATTCAAAATGAAAATTCACATCTT
GATGACATTCCATATAATTTTTTGATTGGTAATGATGGTAAAGTTTATGAAGGAAGAGGT
TTTGAGAAAGAAGGACAACATACTTCAAATTTATATGGATCGAATTATAATTCGATTGAT
TTTATAATTTTATCACAAGACAGTTTAGTTTTTAACAATATAAAATCTGATGCATTAAAT
GAAGCTGTAAGCAAATTGAAAAACTTTTATCCCTTACAAAAAGTGTATCGAAGGGAAGAA
TGGGGTGCAGCCAATCCAAAGGAAGCTCATACAAAATTCAGTCAGAAAAAAGAAATTGCA
TTACTTTCACACTCAGTTACTCAGACTTGCAGTTCCTTTTCTCATTGTGCGACAATAATG
AAAAATATACAAAGAAATCATATGGGTAATAATGGATGGATTGATTTTGCATTTAATTTT
GCTGTTGGAGCAAATGGTTTAATATTTGAATGTCGGGGCTTTGATTTTGTCGGTGCACAT
TTTTCTGCTCTTAATTCAAGATCGATTGGAATTTTAGCAATTGGAGAATTTAATGAAGAT
GAGCCAAGTCAAGAAATGCTTGACACACTTGAAAAATTTCTAGAAGATGCTGCAAAATTA
GGAAAATTATCAGAAGATTTTAAAATACATGGAAGACAAGATTTTGGTTCTTCGGGTCCA
GGAGAAAATATTATGAAACATATCCGAGAATGGTGTCGATATGGTAATAGGACTACTCCA
TGTTAA
>g6528.t1 Gene=g6528 Length=361
MDKNNLVHNNSLNSRKYFQGINRKRNILITIFSVAFILVILTTVSILYFVLKTDSNSDDF
KFENLISRDEWNAAPPKSGIPFLESPIKRIIIAHTAGEFCDNENECKFVVKRIQNENSHL
DDIPYNFLIGNDGKVYEGRGFEKEGQHTSNLYGSNYNSIDFIILSQDSLVFNNIKSDALN
EAVSKLKNFYPLQKVYRREEWGAANPKEAHTKFSQKKEIALLSHSVTQTCSSFSHCATIM
KNIQRNHMGNNGWIDFAFNFAVGANGLIFECRGFDFVGAHFSALNSRSIGILAIGEFNED
EPSQEMLDTLEKFLEDAAKLGKLSEDFKIHGRQDFGSSGPGENIMKHIREWCRYGNRTTP
C
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6528.t1 | CDD | cd06583 | PGRP | 86 | 159 | 2.49834E-17 |
| 12 | g6528.t1 | CDD | cd06583 | PGRP | 222 | 338 | 2.45953E-23 |
| 7 | g6528.t1 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 61 | 189 | 3.4E-30 |
| 8 | g6528.t1 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 190 | 359 | 1.2E-39 |
| 4 | g6528.t1 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 65 | 159 | 3.0E-63 |
| 3 | g6528.t1 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 195 | 354 | 3.0E-63 |
| 1 | g6528.t1 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 85 | 187 | 3.2E-6 |
| 2 | g6528.t1 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 238 | 332 | 1.5E-7 |
| 9 | g6528.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 26 | - |
| 11 | g6528.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 51 | - |
| 10 | g6528.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 52 | 361 | - |
| 15 | g6528.t1 | SMART | SM00701 | pgrp | 63 | 187 | 2.0E-14 |
| 16 | g6528.t1 | SMART | SM00701 | pgrp | 193 | 336 | 8.9E-27 |
| 6 | g6528.t1 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 64 | 158 | 1.83E-24 |
| 5 | g6528.t1 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 194 | 354 | 5.1E-40 |
| 14 | g6528.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 50 | - |
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