Gene loci information

Transcript annotation

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

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 g10465 g10465.t5 isoform g10465.t5 9976896 9979320
chr_1 g10465 g10465.t5 exon g10465.t5.exon1 9976896 9977004
chr_1 g10465 g10465.t5 TSS g10465.t5 9976897 9976897
chr_1 g10465 g10465.t5 cds g10465.t5.CDS1 9976980 9977004
chr_1 g10465 g10465.t5 exon g10465.t5.exon2 9978471 9978595
chr_1 g10465 g10465.t5 cds g10465.t5.CDS2 9978471 9978595
chr_1 g10465 g10465.t5 exon g10465.t5.exon3 9978798 9978906
chr_1 g10465 g10465.t5 cds g10465.t5.CDS3 9978798 9978906
chr_1 g10465 g10465.t5 exon g10465.t5.exon4 9978965 9979000
chr_1 g10465 g10465.t5 cds g10465.t5.CDS4 9978965 9979000
chr_1 g10465 g10465.t5 exon g10465.t5.exon5 9979064 9979320
chr_1 g10465 g10465.t5 cds g10465.t5.CDS5 9979064 9979320
chr_1 g10465 g10465.t5 TTS g10465.t5 9979390 9979390

Sequences

>g10465.t5 Gene=g10465 Length=636
ATCAGTTTCATACAGTGAGTCATTTGTATCACTTCATTTTATTTTTTAATCAAGAAAGCG
AAAAAACTTTTTTTTTTTAAAAAAATGTCCATGTCATTAGAAATTCAAAAAATTTATAGA
TTTTATACTAGAGAAGATTGGAATGCAAGTAAAGCTGAGCCTTATTTTAAATTAATTCAT
CCTATTAAGAGAGTTATTATTTCTCATACAGTCATGAGAGAATGTTATGTTGAGAAAGAA
TGCATATGGATTGTGCAAGAAATACAAAGACTTCATAAAAATTGGGATTTTGGTGATATT
GGATTTAATTTTGTCATCATGAATGATGGAAGCATTTTTGAAGGAAGAGGTTGGGACATT
ATGGGTGCTCATACACGAGGCTTTAATAATAACAGTATAGGTATCGTATACAATGGCAAT
TTTCAAACTCAAAGTCCACCACAAAAGCAAATTCTTGCGGGATTTTCTTTACTTGAAGAA
GGAGTTCGTTTAGGAAAATTATCACCAGATTTTAAAATCTATGGAATGCGACAATTTCAA
AGTAATGAAAGTCCTGGTGAAGCTTTCTTTCAAATGATTAAAACATGGAAAAATTGGTCT
GAAGATATTGATGAATGTTGTCCAAAACCAACATAA

>g10465.t5 Gene=g10465 Length=183
MSMSLEIQKIYRFYTREDWNASKAEPYFKLIHPIKRVIISHTVMRECYVEKECIWIVQEI
QRLHKNWDFGDIGFNFVIMNDGSIFEGRGWDIMGAHTRGFNNNSIGIVYNGNFQTQSPPQ
KQILAGFSLLEEGVRLGKLSPDFKIYGMRQFQSNESPGEAFFQMIKTWKNWSEDIDECCP
KPT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10465.t5 CDD cd06583 PGRP 33 160 0.0000
6 g10465.t5 Gene3D G3DSA:3.40.80.10 Lysozyme 5 178 0.0000
2 g10465.t5 PANTHER PTHR11022 PEPTIDOGLYCAN RECOGNITION PROTEIN 12 171 0.0000
1 g10465.t5 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase 33 158 0.0000
4 g10465.t5 SMART SM00701 pgrp 11 152 0.0000
5 g10465.t5 SMART SM00644 ami_2 19 158 0.0081
3 g10465.t5 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like 11 173 0.0000

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