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.t2 TTS g16550.t2 9904140 9904140
chr_4 g16550 g16550.t2 isoform g16550.t2 9904155 9911172
chr_4 g16550 g16550.t2 exon g16550.t2.exon1 9904155 9904803
chr_4 g16550 g16550.t2 cds g16550.t2.CDS1 9904216 9904782
chr_4 g16550 g16550.t2 TSS g16550.t2 9904808 9904808
chr_4 g16550 g16550.t2 exon g16550.t2.exon2 9911100 9911172

Sequences

>g16550.t2 Gene=g16550 Length=722
TCAAATTTTCGTTCATTTCACGATAAAAATGTATGAAAACTACAAGTTTTTATTGCAGAA
ACTTGTAGATCGATCGAACTTATCAAGAAAAACCATGAAGGTCTTCATCGTTCTTGCCAC
TCTTGCTGTTAGCGCTTTCGCTCAAACACCATGCGATAACATTCGCACACGTTCACAATG
GGGTAGCAGATCAACAAGTCTTACATGGATGCCAACTCAACCACCAACAGGTTTCGCTGT
CCATCATACAGCTGGTGCTCGTTGCACAACCCAAGCTGCTTGTGACACACAAATGAGAAA
TATCCAGAACTTCCACATTAATTCAAATGGCTGGGCTGATATTGGTTACAACTTCTGTGT
TGGTGATCCAGGTCAAATCTATGAAGGTCGTGGTTATGGAAGACAAGGTGCTCATGCTCC
AGGTTTCAATCAACGTGCTTTGGGACACTGCTTCTTTGGTGATCATTCATCAGTCAATCC
AACTGCTGCCGCTTTGTCAAATACACAAGCTTTCATCAATTGTGCCAGAGATCGTGGATT
CTTGTCAGCTGGTCACTGGGTCTCAACCCATCGTGGTGACAGACAAAGCAACACCGCTTG
TCCAGGTCAAGCTCTTCAAAACCAAGTTGCTACATGGCCAAGATTCGTTGCTCAACCTTA
AATTGGATTTTGTGATTGGTTTATTGATGATATTATGGAATTTTAATAAAATTTAAAGAC
TA

>g16550.t2 Gene=g16550 Length=188
MKVFIVLATLAVSAFAQTPCDNIRTRSQWGSRSTSLTWMPTQPPTGFAVHHTAGARCTTQ
AACDTQMRNIQNFHINSNGWADIGYNFCVGDPGQIYEGRGYGRQGAHAPGFNQRALGHCF
FGDHSSVNPTAAALSNTQAFINCARDRGFLSAGHWVSTHRGDRQSNTACPGQALQNQVAT
WPRFVAQP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16550.t2 CDD cd06583 PGRP 43 173 4.25977E-32
6 g16550.t2 Gene3D G3DSA:3.40.80.10 Lysozyme 12 188 7.0E-52
2 g16550.t2 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 17 184 5.7E-52
1 g16550.t2 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 42 171 5.5E-16
8 g16550.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
9 g16550.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
10 g16550.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
11 g16550.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
7 g16550.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 188 -
14 g16550.t2 SMART SM00701 pgrp 21 163 7.6E-37
15 g16550.t2 SMART SM00644 ami_2 34 171 1.0E-11
3 g16550.t2 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 21 186 1.57E-49
5 g16550.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
13 g16550.t2 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 16 -
4 g16550.t2 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

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