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 g6526 g6526.t1 isoform g6526.t1 17482297 17484205
chr_2 g6526 g6526.t1 exon g6526.t1.exon1 17482297 17482610
chr_2 g6526 g6526.t1 cds g6526.t1.CDS1 17482297 17482610
chr_2 g6526 g6526.t1 exon g6526.t1.exon2 17482659 17482752
chr_2 g6526 g6526.t1 cds g6526.t1.CDS2 17482659 17482752
chr_2 g6526 g6526.t1 exon g6526.t1.exon3 17482810 17482934
chr_2 g6526 g6526.t1 cds g6526.t1.CDS3 17482810 17482934
chr_2 g6526 g6526.t1 exon g6526.t1.exon4 17482997 17483366
chr_2 g6526 g6526.t1 cds g6526.t1.CDS4 17482997 17483366
chr_2 g6526 g6526.t1 exon g6526.t1.exon5 17483428 17483924
chr_2 g6526 g6526.t1 cds g6526.t1.CDS5 17483428 17483924
chr_2 g6526 g6526.t1 exon g6526.t1.exon6 17483980 17484205
chr_2 g6526 g6526.t1 cds g6526.t1.CDS6 17483980 17484205
chr_2 g6526 g6526.t1 TSS g6526.t1 17484241 17484241
chr_2 g6526 g6526.t1 TTS g6526.t1 NA NA

Sequences

>g6526.t1 Gene=g6526 Length=1626
ATGGAAGTAACAAACAACGAAATTATTGAACGATATCAGCCATTTCCAACGTTTGAAAAT
TCTGAATATTTTCAGCAAAATGGAGATATACAAAACTATGAAGATATAACTAGAAATACT
GCTTTAAAAATTCCAGTTAATAATCAAAAAGCAATAGTTGCTGTTAGTAGTGAAGACATT
CATGTTGGCAACATAATTTATTACCACGTCCAAAATCAAATGAAAATGCAAAATATGAAA
GTTGAAAAAACTTCAGAGAAAATTCCAGAAAATGAAACAAGTTCTTCAAAAATGTCAAGT
GATTTTGATAACAATTCAAAGTTAAATAAATGGTTCAATAGGGAAAATAACAAAAGAAAC
ATTTTGATAACGACAATCGCACTGTTTGGGATATCTTTAAGTGCATTAATCATTTACATT
GTTATTTTGTCTGATACCAGTGAAAACAATTACACTTCAACGACGTCAAAAATTATCACT
GACGATGATATAACAACAACAATTCCATTAACAACAACAACAACAACAACGTTATCAGAA
TCTACAAGCACCACTTTAATTTCAACAACTACAATTGCATATCAAGATATTCCTTTACCA
GATTTCTTAATTTCAAGAGACGAATGGAATGCTAATCCAACAAATTCAAATATTTCTAGA
TTACATTTTCCTATTAAGAGAATTATTATAGCACACACCGGTGGAAGATATTGTTTTGAA
GAGATTGATTGCAAAAATCTTGTTAAAGAAATTCAAAATGAAAATTCACATCTTGATGAT
ATTCCATACAATTATCTTATAGGTGAAGATGGAAAAATTTATGAAGGAAGAGGTTTTGAA
TTTCAAGGAGAACATACTTCAAATTTATATGGAACTGAATTTAATTCGATTGGTATTTGT
ATTGCATTTATGGGAAATTATCAATCATTATCTCCTATATTAACTCCTTTAATAAAGTTT
ATTGACTATTATCTCTCATACAAAGTAATTGATGAAGATTATAAACTTTTTTCACAAGAT
GATTTGATAATTAGGGATGATAAAGCTTATGCATTAAAGGATGCAATCAAAGGAATGGAT
AATTTTTATGAATTACGAAAAATTATAAGAAGAGAAGAATGGAATGCAGATATTCCACGA
GATGAACAAATAAAGTTTAATCGTATCATGGATATGGCAATGTTAGCTCATACAGTTACA
AATAGATGCTTTACTATCAATGAATGTGCAGCAATTGGTCAACAGATTCAAAACAAAAGT
TTTGAAGATGGTTTAATAGATTTCAAATATGGTTTTATTATTGGAAATAATGGACTAGTA
TTTGAGGGTCGAGGGTGGGATGTGATTGGTGAACATACACCTAATTATGATTCAATTTCT
GTTGGAATAGCAGTTATAGGAAATTATGATAACACTGAACCGTATAAATCAATGTACACC
ACGCTTGCTGATTTTCTAGACGATAGTTATGCTCTAGGAAAATTAACAGATGATTACAAA
TTGCACGGACAAATTGATTTTGGGGGATCTGGACCTGGAAGAGAATTTTTTAACAATATT
CTTAATTGGTGTCGATATGGAAATAGAACAACTTCTTCAGAAACTCCTTGTATTTCCACA
AGATAA

>g6526.t1 Gene=g6526 Length=541
MEVTNNEIIERYQPFPTFENSEYFQQNGDIQNYEDITRNTALKIPVNNQKAIVAVSSEDI
HVGNIIYYHVQNQMKMQNMKVEKTSEKIPENETSSSKMSSDFDNNSKLNKWFNRENNKRN
ILITTIALFGISLSALIIYIVILSDTSENNYTSTTSKIITDDDITTTIPLTTTTTTTLSE
STSTTLISTTTIAYQDIPLPDFLISRDEWNANPTNSNISRLHFPIKRIIIAHTGGRYCFE
EIDCKNLVKEIQNENSHLDDIPYNYLIGEDGKIYEGRGFEFQGEHTSNLYGTEFNSIGIC
IAFMGNYQSLSPILTPLIKFIDYYLSYKVIDEDYKLFSQDDLIIRDDKAYALKDAIKGMD
NFYELRKIIRREEWNADIPRDEQIKFNRIMDMAMLAHTVTNRCFTINECAAIGQQIQNKS
FEDGLIDFKYGFIIGNNGLVFEGRGWDVIGEHTPNYDSISVGIAVIGNYDNTEPYKSMYT
TLADFLDDSYALGKLTDDYKLHGQIDFGGSGPGREFFNNILNWCRYGNRTTSSETPCIST
R

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g6526.t1 CDD cd06583 PGRP 224 342 1.02622E-20
15 g6526.t1 CDD cd06583 PGRP 391 510 1.55102E-19
10 g6526.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 202 349 6.8E-34
9 g6526.t1 Gene3D G3DSA:3.40.80.10 Lysozyme 365 528 5.1E-33
3 g6526.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 55 362 7.0E-64
5 g6526.t1 PANTHER PTHR11022:SF67 PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED 55 362 7.0E-64
4 g6526.t1 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 367 526 7.0E-64
6 g6526.t1 PANTHER PTHR11022:SF67 PEPTIDOGLYCAN-RECOGNITION PROTEIN LB-RELATED 367 526 7.0E-64
2 g6526.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 224 308 4.8E-7
1 g6526.t1 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 391 500 3.8E-7
11 g6526.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 120 -
13 g6526.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 142 -
12 g6526.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 541 -
18 g6526.t1 SMART SM00701 pgrp 203 343 2.9E-24
17 g6526.t1 SMART SM00701 pgrp 366 508 2.7E-25
8 g6526.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 203 364 8.35E-31
7 g6526.t1 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 367 526 6.48E-34
16 g6526.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -

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