Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peptidoglycan recognition protein 4.

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_2 g6530 g6530.t1 isoform g6530.t1 17492883 17495027
chr_2 g6530 g6530.t1 exon g6530.t1.exon1 17492883 17493172
chr_2 g6530 g6530.t1 cds g6530.t1.CDS1 17492883 17493172
chr_2 g6530 g6530.t1 exon g6530.t1.exon2 17493232 17493328
chr_2 g6530 g6530.t1 cds g6530.t1.CDS2 17493232 17493328
chr_2 g6530 g6530.t1 exon g6530.t1.exon3 17493379 17493503
chr_2 g6530 g6530.t1 cds g6530.t1.CDS3 17493379 17493503
chr_2 g6530 g6530.t1 exon g6530.t1.exon4 17493559 17493934
chr_2 g6530 g6530.t1 cds g6530.t1.CDS4 17493559 17493934
chr_2 g6530 g6530.t1 exon g6530.t1.exon5 17493989 17494380
chr_2 g6530 g6530.t1 cds g6530.t1.CDS5 17493989 17494380
chr_2 g6530 g6530.t1 exon g6530.t1.exon6 17494778 17495027
chr_2 g6530 g6530.t1 cds g6530.t1.CDS6 17494778 17495027
chr_2 g6530 g6530.t1 TSS g6530.t1 17495063 17495063
chr_2 g6530 g6530.t1 TTS g6530.t1 NA NA

Sequences

>g6530.t1 Gene=g6530 Length=1530
ATGGAAGCAACAAATAGCAATATTATTGAAAGACGTCGACCAATTCGACGGAATGATTCA
ATTTCTACAATTGCGAGCTCAGCAGCAGCTGCACAAATGCAACAATTTACATCTACAAAC
AGCTATGGATTACCAAATGATAATCAAATTATTCCAACAAATAGTCAAACTAGTATGCGC
TTTGATAACAGCGAAGGCGTTCATGTTGGCAATATAATTTATCATAATTATTACCAAAAT
CCTCCGGAAATTTTAAGTGATAAAAAGATACAAGAAAACTCTTTAATAAGTTCAAGCACC
TCTGAGAGCTCTTTTAAAAAGCGTAATTGCTTTAGCAGTGAAAATAAAAGAAAAAGAATT
TTGATAACAGTAATTGTGATAAGCTTGGTTTTAGCAATATCGATAGTCATTCCAATCACC
TACTTTTTACTTACTAATAATCCTTCCGAGAAAAATGGTGATAACGATAGTACGACTTCT
CCCTCAACCACTTATGTAACAACAACTCCTTTGCCAACGAGTTTCTTAATTAAAAGAAAT
GAATGGAATGCAAATGAACCCAAATCAGATATTAAAAAATTAAATCAACCTATTAAAAGA
ATTATCATTGGACATACCGGTGGAAATTTTTGTAACAATACAGATGAATGTAGATTGCTT
GTGAAACAAATACAAGTCGAAAATTCACATCTTGATGATATTCCATACAATTATCTTATA
GGTGGTGATGGAAAAGTTTATGAAGGAAGAGGATTTGAATTTGAAGGACAACACACAGCA
AATTTACATGGAACTGAATTTAATTCTATAGGAATTTGTATTGCATTCATTGGAAATTAT
AATGTAACGTCACCAAATGAGAATCAATTAAACGTTTTAAGAGAGTTTATTAATCATTTT
ATTTCAAAAGAATTATCAGAAGATTATATTATAATAAAACAGGATGATTTAATATATAAA
AGCACAAAGGCAAATGCTTTAAATGAAGCTATCGTCAATTTTGAGAACTACTATGCATTG
CAAACAGTGTATCGAAGAGAAGAATGGGGTGCACTTGAACCGTCTGGAAAACTTGAAAAA
TTTAATAAAATAATGGATTTGACTTTGTTATCACATACGATTACAGATTCATGCAGTTCT
ATGTCATATTGTTCTCAGTTAATGAGGACAATGCAACAAACTAACATGAACAAAAATGGA
TTTCTTGACTATGGTTTTAATTTTGCTATTGGAGGGAATGGATTGATTTTTGAAGGACGA
GGTTTTGACAATGTCGGAGCTCATTTAAAAATTTTGAATTCAAAATCAATTGGAATTGCA
GCAATTGGAGATTTTGATAAAAATGAACCAAGTTTAGAAATGCTTGACACACTTGTTAAG
TTCTTAGAAGATGCTGTAAAATTAGGGAAATTAACACAAGATTATAGAGTTAATGGAAGG
CAAGATTTTGGTTGGGAAGGTCCAGGAAAAAACATCATGAAATTTATTAGAGAATGGTGT
CGTTATGGTAATAGGACTACTCCATGTTAA

>g6530.t1 Gene=g6530 Length=509
MEATNSNIIERRRPIRRNDSISTIASSAAAAQMQQFTSTNSYGLPNDNQIIPTNSQTSMR
FDNSEGVHVGNIIYHNYYQNPPEILSDKKIQENSLISSSTSESSFKKRNCFSSENKRKRI
LITVIVISLVLAISIVIPITYFLLTNNPSEKNGDNDSTTSPSTTYVTTTPLPTSFLIKRN
EWNANEPKSDIKKLNQPIKRIIIGHTGGNFCNNTDECRLLVKQIQVENSHLDDIPYNYLI
GGDGKVYEGRGFEFEGQHTANLHGTEFNSIGICIAFIGNYNVTSPNENQLNVLREFINHF
ISKELSEDYIIIKQDDLIYKSTKANALNEAIVNFENYYALQTVYRREEWGALEPSGKLEK
FNKIMDLTLLSHTITDSCSSMSYCSQLMRTMQQTNMNKNGFLDYGFNFAIGGNGLIFEGR
GFDNVGAHLKILNSKSIGIAAIGDFDKNEPSLEMLDTLVKFLEDAVKLGKLTQDYRVNGR
QDFGWEGPGKNIMKFIREWCRYGNRTTPC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6530.t1 CDD cd06583 PGRP 197 317 9.58264E-23
14 g6530.t1 CDD cd06583 PGRP 370 483 7.64335E-25
9 g6530.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 175 337 2.4E-33
10 g6530.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 343 503 1.0E-36
4 g6530.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 174 337 2.0E-74
6 g6530.t1 PANTHER PTHR11022:SF67 PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED 174 337 2.0E-74
3 g6530.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 343 502 2.0E-74
5 g6530.t1 PANTHER PTHR11022:SF67 PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED 343 502 2.0E-74
1 g6530.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 196 303 4.0E-9
2 g6530.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 370 488 1.4E-8
11 g6530.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 119 -
13 g6530.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 144 -
12 g6530.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 145 509 -
17 g6530.t1 SMART SM00701 pgrp 174 318 2.6E-31
18 g6530.t1 SMART SM00701 pgrp 341 484 1.9E-28
8 g6530.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 176 338 7.59E-35
7 g6530.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 342 502 2.62E-38
16 g6530.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 120 142 -

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