General information for g5768.t1
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 g5768 is located on chr_2: 11818728..11820327 (+ 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 | g5768 | g5768.t1 | TSS | g5768.t1 | 11818614 | 11818614 |
| chr_2 | g5768 | g5768.t1 | isoform | g5768.t1 | 11818728 | 11820327 |
| chr_2 | g5768 | g5768.t1 | exon | g5768.t1.exon1 | 11818728 | 11819235 |
| chr_2 | g5768 | g5768.t1 | cds | g5768.t1.CDS1 | 11818728 | 11819235 |
| chr_2 | g5768 | g5768.t1 | exon | g5768.t1.exon2 | 11819464 | 11819673 |
| chr_2 | g5768 | g5768.t1 | cds | g5768.t1.CDS2 | 11819464 | 11819673 |
| chr_2 | g5768 | g5768.t1 | exon | g5768.t1.exon3 | 11819743 | 11819876 |
| chr_2 | g5768 | g5768.t1 | cds | g5768.t1.CDS3 | 11819743 | 11819876 |
| chr_2 | g5768 | g5768.t1 | exon | g5768.t1.exon4 | 11819935 | 11820327 |
| chr_2 | g5768 | g5768.t1 | cds | g5768.t1.CDS4 | 11819935 | 11820327 |
| chr_2 | g5768 | g5768.t1 | TTS | g5768.t1 | 11820607 | 11820607 |
Sequences
>g5768.t1 Gene=g5768 Length=1245
ATGTCAAAATCAGATGATATGGAGCACATGGAGCTTGATATGGCAATTCCAACGAGTTTT
GATAAAATCAATGAATATTATCGTGATAATTTAAAAAATATTTTAAAATCAAGCTCAAGT
GAAACAGTGTCATCAATTACGTCGACAGAGAGAAAGAAAAAAATGTCTGTCAATGATTAT
GACGATAGTTCATCGATAGCATCAGATTCTGATTTTGAAGATTGTACAAATTGCAAAAAA
TCAAACGATCAAGTGATCGTCAATGTCAACGAAAATTGTTCAAGTGCCTTATCAAATGAT
GGGATTTCAGCCACAACAACTGTTTGTGATAATTTGCAAAATAAACTACAAAACATAAAT
TCTGTTTCTATAAATCATTCGTCAGATGTTCACTTTGGAAATAAAACTTTTTTTAATGGA
CCTGTTACTATTAAACAAATTGTGATAAAAGATGAATATTTAAGGAAGAAGGATGACAGT
AATGGTGTACTCAACAGTGGCTTTGAAGGATCATCAACTCAAATAAATACAAATCACATC
ACAAATGATAAAAGTGATGACATCAAACAAGAAAATACAGTACAAAACTCAAATGATTGT
GAAAGCAATAAAAAAATTGTGATAGCTCAAAAAAAAATTATGCTTGCTCTAGTCCTTACT
GTTTGTGCACTTGCAGCAGCGCTATCATTATTATTTATTGTTTTACCATACAATGAAGAC
GAGGAACCGCCTCATATTATAACAAGAGATAAATGGCAAGCGAAAACGCCAAAAGAAGCT
CTCACAAAATTAGAATTGCCGGTAAAACGAATTATAATCGCTCATACTGTAACAGATGAA
TGTTTTACTGAGGAAGATTGTGCTCAAATTGTTCGCGATATTCAAAATATGCATTTATAT
AACTATCAATTTAATTTCTCCGATATTGCTTATAATTTTATTATCGGAGGGGATGGTTCA
ATTTTTGAAGGTAGAGGATGGAGAGATCAGGGAGCACATACAAGTGGATATAATCGTGGA
AGCATAGGTGTTGCATATATTGGCACTTTTATCGACAAAGTACCAAGTAATATGCAGTTG
AATGCGGGTTTTCGCTTATTTCATGAAGGCGTTAGAGTAGGTGCACTTACAAGTGATTAC
GTGATTTTTGGCGCCTCTCAATTAAGAACAACACAAAGTCCTGGTGATGCCTTTTTTGAG
CTTATCAAAAAATGGAAACATTTTTCAGAGACTATTGTGTCTTAA
>g5768.t1 Gene=g5768 Length=414
MSKSDDMEHMELDMAIPTSFDKINEYYRDNLKNILKSSSSETVSSITSTERKKKMSVNDY
DDSSSIASDSDFEDCTNCKKSNDQVIVNVNENCSSALSNDGISATTTVCDNLQNKLQNIN
SVSINHSSDVHFGNKTFFNGPVTIKQIVIKDEYLRKKDDSNGVLNSGFEGSSTQINTNHI
TNDKSDDIKQENTVQNSNDCESNKKIVIAQKKIMLALVLTVCALAAALSLLFIVLPYNED
EEPPHIITRDKWQAKTPKEALTKLELPVKRIIIAHTVTDECFTEEDCAQIVRDIQNMHLY
NYQFNFSDIAYNFIIGGDGSIFEGRGWRDQGAHTSGYNRGSIGVAYIGTFIDKVPSNMQL
NAGFRLFHEGVRVGALTSDYVIFGASQLRTTQSPGDAFFELIKKWKHFSETIVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5768.t1 | CDD | cd06583 | PGRP | 267 | 397 | 8.50513E-37 |
| 5 | g5768.t1 | Gene3D | G3DSA:3.40.80.10 | Lysozyme | 237 | 412 | 6.5E-51 |
| 13 | g5768.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 60 | - |
| 2 | g5768.t1 | PANTHER | PTHR11022 | PEPTIDOGLYCAN RECOGNITION PROTEIN | 113 | 410 | 5.2E-64 |
| 3 | g5768.t1 | PANTHER | PTHR11022:SF68 | PEPTIDOGLYCAN-RECOGNITION PROTEIN LF | 113 | 410 | 5.2E-64 |
| 1 | g5768.t1 | Pfam | PF01510 | N-acetylmuramoyl-L-alanine amidase | 267 | 395 | 5.6E-11 |
| 6 | g5768.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 212 | - |
| 8 | g5768.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 213 | 237 | - |
| 7 | g5768.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 238 | 414 | - |
| 11 | g5768.t1 | SMART | SM00701 | pgrp | 244 | 389 | 1.4E-54 |
| 12 | g5768.t1 | SMART | SM00644 | ami_2 | 256 | 395 | 1.1E-4 |
| 4 | g5768.t1 | SUPERFAMILY | SSF55846 | N-acetylmuramoyl-L-alanine amidase-like | 244 | 410 | 1.7E-55 |
| 10 | g5768.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 213 | 235 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5768/g5768.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5768.t1.fa.iupred3.txt does not exist
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 transcript has been annotated with K01446 (peptidoglycan recognition protein)
Pathway
- This transcript belongs to the following pathways
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.
