General information for g6529.t3
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 g6529 is located on chr_2: 17490748..17491982 (- 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 | g6529 | g6529.t3 | TTS | g6529.t3 | 17490077 | 17490077 |
| chr_2 | g6529 | g6529.t3 | isoform | g6529.t3 | 17490748 | 17491982 |
| chr_2 | g6529 | g6529.t3 | exon | g6529.t3.exon1 | 17490748 | 17490782 |
| chr_2 | g6529 | g6529.t3 | cds | g6529.t3.CDS1 | 17490748 | 17490782 |
| chr_2 | g6529 | g6529.t3 | exon | g6529.t3.exon2 | 17490841 | 17491216 |
| chr_2 | g6529 | g6529.t3 | cds | g6529.t3.CDS2 | 17490841 | 17491216 |
| chr_2 | g6529 | g6529.t3 | exon | g6529.t3.exon3 | 17491272 | 17491660 |
| chr_2 | g6529 | g6529.t3 | cds | g6529.t3.CDS3 | 17491272 | 17491660 |
| chr_2 | g6529 | g6529.t3 | exon | g6529.t3.exon4 | 17491718 | 17491982 |
| chr_2 | g6529 | g6529.t3 | cds | g6529.t3.CDS4 | 17491718 | 17491982 |
| chr_2 | g6529 | g6529.t3 | TSS | g6529.t3 | 17492018 | 17492018 |
Sequences
>g6529.t3 Gene=g6529 Length=1065
ATGGAAGCAATAAATAGTGATGTTATTGAAAGACGTCGACCAATTCGACGGAATGACTCT
ATGTCTACAATTGCGAGTTCAGCTGCAGCTGCACAAGTTCAACACATAGAAAATATGCAG
CAAGTGCAGCAATTCACCACTTTAAATAACAATGATAATCAAATTTTTCCAACAAATAAC
CAAACTAGCTTAAAATTTGAAAACAGTGAAGGAGTTCATGTTGGCAATATAATTAACCAC
TATTATCAGACTGTACCACCTATAGTTTTAAACAATAAAGAAGCACGAAAAAGTTCTCAA
AGTAACTCAAGCTTAACAGAATCATTCAAAATTGCGAAAAAATGTTTTATCAGCAATAAT
AGAAGAAGAAATGTTTTGATAATAGCAATCACGATAAGCACTGTTGTATTGATATCAATT
ATTATTCCAATTATATATTTCACACTCACTGATAATGACAAAAATAACAATCCAGATGAT
AATACTACTACTATTACAACTTCTACTACTTCTGCATCCGAAGTGCCTTCAGATTTATTA
ATTACAAGAGAAGAATGGAATGCAGATAGTCCCAAAGATGGGATTAAAAAATTAATTGGA
CCAATAAAAAGAATTATTGTAGCTCATACAGGAGGAAATTCATGCAATACTATGGATGAA
TGTAAAACACTTGTGAAAAAAATTCAAACAGAAAATTCAGACCTTGATGATATTCCATAT
AATTTTTTGATTGGTAATGATGGAAAAGTTTATGAAGGAAGAGGGTTTGAGTTTCAAGGA
CAACATACTTCAAATTTATATGGTACTGAATTTAATTCAATTGGAATTTGTATTGCATTT
ATTGGAAATTATAATACAACTTCACTAACTGAAGACCAGTTGAGAATTTTCACTGACTTT
ATTAACCATTATATTTCAAAAGATGTATCAGAAGATTATTTAATATTTTCTCAAGATGAT
TTAATGAATACAGATATTAAATCTAGTGCTCTAAATGAAGCCTTTTCAAATTTTGAAAAT
TTTTTACCTCTTCATCCAATTTTTAAAAGAAAAGACTGGTCCACT
>g6529.t3 Gene=g6529 Length=355
MEAINSDVIERRRPIRRNDSMSTIASSAAAAQVQHIENMQQVQQFTTLNNNDNQIFPTNN
QTSLKFENSEGVHVGNIINHYYQTVPPIVLNNKEARKSSQSNSSLTESFKIAKKCFISNN
RRRNVLIIAITISTVVLISIIIPIIYFTLTDNDKNNNPDDNTTTITTSTTSASEVPSDLL
ITREEWNADSPKDGIKKLIGPIKRIIVAHTGGNSCNTMDECKTLVKKIQTENSDLDDIPY
NFLIGNDGKVYEGRGFEFQGQHTSNLYGTEFNSIGICIAFIGNYNTTSLTEDQLRIFTDF
INHYISKDVSEDYLIFSQDDLMNTDIKSSALNEAFSNFENFLPLHPIFKRKDWST
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g6529.t3 | CDD | cd06583 | PGRP | 201 | 295 | 6.48145E-23 |
| 5 | g6529.t3 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 179 | 341 | 5.0E-34 |
| 2 | g6529.t3 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 58 | 341 | 2.4E-33 |
| 3 | g6529.t3 | PANTHER | PTHR11022:SF67 | PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED | 58 | 341 | 2.4E-33 |
| 1 | g6529.t3 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 201 | 299 | 3.3E-9 |
| 6 | g6529.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 124 | - |
| 8 | g6529.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 149 | - |
| 7 | g6529.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 150 | 355 | - |
| 11 | g6529.t3 | SMART | SM00701 | pgrp | 178 | 322 | 8.8E-32 |
| 4 | g6529.t3 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 180 | 343 | 3.01E-34 |
| 10 | g6529.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
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