Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Lysozyme c-1.

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_3 g1249 g1249.t3 TSS g1249.t3 9121509 9121509
chr_3 g1249 g1249.t3 isoform g1249.t3 9121543 9122308
chr_3 g1249 g1249.t3 exon g1249.t3.exon1 9121543 9121828
chr_3 g1249 g1249.t3 cds g1249.t3.CDS1 9121543 9121828
chr_3 g1249 g1249.t3 exon g1249.t3.exon2 9121891 9122095
chr_3 g1249 g1249.t3 cds g1249.t3.CDS2 9121891 9122033
chr_3 g1249 g1249.t3 exon g1249.t3.exon3 9122182 9122308
chr_3 g1249 g1249.t3 TTS g1249.t3 9122317 9122317

Sequences

>g1249.t3 Gene=g1249 Length=618
ATGAAAACTTTAATTTTTACAACTTTATTTGTTGCATTTTTCGCTTATACAAATGCGAAA
ATTTATTCAAAATGTGAACTTGTGGAAGAATTGCATAATGCTGGATTTCCGAAAGAAGAT
TTACCAGATTGGGTATGTTTAGTTGAGCATGAAAGTAATTATGATTCAGAAGCTATCGGT
GAAGAAAATCATGATGGATCTCAAGATTATGGCATTTTTCAAATCAATTCAAAATACTGG
TGTAATGTTGGTTCTCCTGGTGGAGACTGCAATTTGGATTGCAATTCTCTCATTAGTGAT
GACATAGGTGATGACATTCAATGTGCAAAAATGATTTTTGATCGTCATCATTTTGATGCA
TGGTATGGTTGGATCAATAACTGCAAAGGTGCTGAGCTTCCTTCAATTGATGAATGCAAT
GTTAAATAGAAATATTTTTCTTTCGTTGTCAAAATATTTTTATTTTCTTTTAAAAACAAT
TTACAAAATTTTTAAAGAGAATGAATGAATTCTAAATAAAACAGAGACATTTTTTAATAG
TCAACTTGCACAAAATTATGCGACTACCAGTCAAGTATGCATGCAAGTGCCAGAGCTTAC
TATGATATAATAAACATA

>g1249.t3 Gene=g1249 Length=142
MKTLIFTTLFVAFFAYTNAKIYSKCELVEELHNAGFPKEDLPDWVCLVEHESNYDSEAIG
EENHDGSQDYGIFQINSKYWCNVGSPGGDCNLDCNSLISDDIGDDIQCAKMIFDRHHFDA
WYGWINNCKGAELPSIDECNVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g1249.t3 CDD cd16899 LYZ_C_invert 20 139 2.88032E-66
15 g1249.t3 Gene3D G3DSA:1.10.530.10 - 16 140 1.6E-48
2 g1249.t3 PANTHER PTHR11407 LYSOZYME C 1 140 3.9E-51
3 g1249.t3 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 1 140 3.9E-51
12 g1249.t3 PRINTS PR00137 Lysozyme signature 21 39 4.7E-5
7 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 1.0E-19
6 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 1.0E-19
8 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 67 83 1.0E-19
5 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 88 97 1.0E-19
10 g1249.t3 PRINTS PR00137 Lysozyme signature 95 110 4.7E-5
4 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 98 113 1.0E-19
11 g1249.t3 PRINTS PR00137 Lysozyme signature 116 125 4.7E-5
9 g1249.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 117 128 1.0E-19
1 g1249.t3 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 139 9.5E-34
17 g1249.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
18 g1249.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
19 g1249.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
20 g1249.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
16 g1249.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 142 -
23 g1249.t3 ProSitePatterns PS00128 Glycosyl hydrolases family 22 (GH22) domain signature. 90 108 -
24 g1249.t3 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 142 36.82
22 g1249.t3 SMART SM00263 lysozyme-fin 20 140 3.9E-51
13 g1249.t3 SUPERFAMILY SSF53955 Lysozyme-like 19 139 9.92E-45
14 g1249.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -

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:0003796 lysozyme activity MF

KEGG

Orthology

Pathway

This gene does not belong to any 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