Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peptidoglycan-recognition protein SC2.

Parent gene

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 g9460 g9460.t1 TTS g9460.t1 3190209 3190209
chr_1 g9460 g9460.t1 isoform g9460.t1 3190261 3190824
chr_1 g9460 g9460.t1 exon g9460.t1.exon1 3190261 3190824
chr_1 g9460 g9460.t1 cds g9460.t1.CDS1 3190261 3190824
chr_1 g9460 g9460.t1 TSS g9460.t1 3190847 3190847

Sequences

>g9460.t1 Gene=g9460 Length=564
ATGAAGCTTTTAATTGTGCTTGCTTTTGTGGCCTTTGCATCGGCCCAAACTCCATGTCAA
AACATTCGTACAAGAGCTCAATGGGGCTCACGCTCAACTAGCTTAACATGGATGGCTACA
CGTCCACCAAGTGGTTTTGCAATTCATCATACAGCCGGTGCTCGTTGCACGACTCAAGCA
GCTTGTGATACTCAAATGAGAAATATTCAAAACTTCCACATGAATACAAACGGTTGGGCT
GATATTGGTTACAATTTCTGCATTGGTGATCCAGGTCAAGTTTATGAAGGAAGAGGTTAT
GGTCGACATGGAGCCCATGCTCCAGGTTTCAATGCACGTGCTTTGGGTCACTGCTTCTTT
GGTGATCATTCAAACGTCCTTCCAACTGCTGCCGCTTTAAGTAATACTCAAGCATTCATC
ACTTGCTCACGTAATAATGGTGAACTTACTTCTGGACACTGGGTATCAACTCATAGAAAC
GATCGTCAAAGTGCAACTGCTTGTCCTGGACAAGCCTTGTTCAACACTGTCTCAACTTGG
GATCGCTTCCATTCAAATCCCTAA

>g9460.t1 Gene=g9460 Length=187
MKLLIVLAFVAFASAQTPCQNIRTRAQWGSRSTSLTWMATRPPSGFAIHHTAGARCTTQA
ACDTQMRNIQNFHMNTNGWADIGYNFCIGDPGQVYEGRGYGRHGAHAPGFNARALGHCFF
GDHSNVLPTAAALSNTQAFITCSRNNGELTSGHWVSTHRNDRQSATACPGQALFNTVSTW
DRFHSNP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g9460.t1 CDD cd06583 PGRP 42 172 5.1266E-32
6 g9460.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 11 187 2.3E-52
2 g9460.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 12 183 1.8E-52
1 g9460.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 41 170 2.1E-15
8 g9460.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
9 g9460.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
10 g9460.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 10 -
11 g9460.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 15 -
7 g9460.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 187 -
14 g9460.t1 SMART SM00701 pgrp 20 162 1.6E-37
15 g9460.t1 SMART SM00644 ami_2 33 170 4.8E-8
3 g9460.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 19 185 1.57E-50
5 g9460.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 15 -
13 g9460.t1 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 15 -
4 g9460.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 21 -

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

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. There were no conditions that were differentially expressed