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_4 g16550 g16550.t3 TTS g16550.t3 9904140 9904140
chr_4 g16550 g16550.t3 isoform g16550.t3 9904216 9904782
chr_4 g16550 g16550.t3 exon g16550.t3.exon1 9904216 9904385
chr_4 g16550 g16550.t3 cds g16550.t3.CDS1 9904216 9904385
chr_4 g16550 g16550.t3 exon g16550.t3.exon2 9904470 9904782
chr_4 g16550 g16550.t3 cds g16550.t3.CDS2 9904470 9904782
chr_4 g16550 g16550.t3 TSS g16550.t3 9904808 9904808

Sequences

>g16550.t3 Gene=g16550 Length=483
ATGAAGGTCTTCATCGTTCTTGCCACTCTTGCTGTTAGCGCTTTCGCTCAAACACCATGC
GATAACATTCGCACACGTTCACAATGGGGTAGCAGATCAACAAGTCTTACATGGATGCCA
ACTCAACCACCAACAGGTTTCGCTGTCCATCATACAGCTGGTGCTCGTTGCACAACCCAA
GCTGCTTGTGACACACAAATGAGAAATATCCAGAACTTCCACATTAATTCAAATGGCTGG
GCTGATATTGGTTACAACTTCTGTGTTGGTGATCCAGGTCAAATCTATGAAGGTCGTGGT
TATGGAAGACAAGCTTTGTCAAATACACAAGCTTTCATCAATTGTGCCAGAGATCGTGGA
TTCTTGTCAGCTGGTCACTGGGTCTCAACCCATCGTGGTGACAGACAAAGCAACACCGCT
TGTCCAGGTCAAGCTCTTCAAAACCAAGTTGCTACATGGCCAAGATTCGTTGCTCAACCT
TAA

>g16550.t3 Gene=g16550 Length=160
MKVFIVLATLAVSAFAQTPCDNIRTRSQWGSRSTSLTWMPTQPPTGFAVHHTAGARCTTQ
AACDTQMRNIQNFHINSNGWADIGYNFCVGDPGQIYEGRGYGRQALSNTQAFINCARDRG
FLSAGHWVSTHRGDRQSNTACPGQALQNQVATWPRFVAQP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g16550.t3 CDD cd06583 PGRP 43 145 4.5023E-19
7 g16550.t3 Gene3D G3DSA:3.40.80.10 Lysozyme 14 106 3.4E-27
8 g16550.t3 Gene3D G3DSA:3.40.80.10 Lysozyme 107 160 4.2E-5
2 g16550.t3 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 17 100 3.3E-34
3 g16550.t3 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 104 156 3.3E-34
1 g16550.t3 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 42 101 1.2E-5
10 g16550.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
11 g16550.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g16550.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
13 g16550.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
9 g16550.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 160 -
16 g16550.t3 SMART SM00701 pgrp 21 135 1.2E-13
4 g16550.t3 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 21 158 7.85E-36
6 g16550.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
15 g16550.t3 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 16 -
5 g16550.t3 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 16 -

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