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_2 g8477 g8477.t2 TSS g8477.t2 30879852 30879852
chr_2 g8477 g8477.t2 isoform g8477.t2 30879999 30887780
chr_2 g8477 g8477.t2 exon g8477.t2.exon1 30879999 30880000
chr_2 g8477 g8477.t2 exon g8477.t2.exon2 30886407 30886656
chr_2 g8477 g8477.t2 cds g8477.t2.CDS1 30886527 30886656
chr_2 g8477 g8477.t2 exon g8477.t2.exon3 30886745 30886897
chr_2 g8477 g8477.t2 cds g8477.t2.CDS2 30886745 30886897
chr_2 g8477 g8477.t2 exon g8477.t2.exon4 30886995 30887075
chr_2 g8477 g8477.t2 cds g8477.t2.CDS3 30886995 30887075
chr_2 g8477 g8477.t2 exon g8477.t2.exon5 30887140 30887187
chr_2 g8477 g8477.t2 cds g8477.t2.CDS4 30887140 30887187
chr_2 g8477 g8477.t2 exon g8477.t2.exon6 30887466 30887780
chr_2 g8477 g8477.t2 cds g8477.t2.CDS5 30887466 30887482
chr_2 g8477 g8477.t2 TTS g8477.t2 30887790 30887790

Sequences

>g8477.t2 Gene=g8477 Length=849
AATAGCACATTTGTCTGATTAATTCATGGCACATTCTGAAATTTATTTCATCTTTATATT
TTTATTCCTATACAATTTGTTCTTTAAATCGTGACCGCTGTAGTCTACTTAGAAAATCAA
CGATGATGATGAGGTACCTGGAGTTGTTATTATTATTGCTAGTTGTTACAACAGATGCCA
AAATATTCACAAGATGTGAATTAGCAAAGGAACTTTTCAATAGTGGCATTCCAAAGACAT
TCATCTCAAATTGGGTTTGCTTGATCGAGGCAGAATCAGGTGCTGACACATCAAAAGTTA
CAGAATTTCCGAATCTAAGTGCCAGTTATGGGATATTTCAGATAAACTCAAAAGAATGGT
GCCGTAAATCGCGAAAAGGAGGCGAGTGTGGGACGCGTTGTGAAGACTTTTTAACTGAAG
ATATTAAAAATGATATAAGATGCGCTAAAGTCATATACAATCGTCATGGATTTTCATATT
GGAAAGGTTGGACATCACGATGCAAATCTCGTCCATTACCTGATGTGTCAAAATGCTTTG
GCAGAAAGTAAGAAAAATGCAAATAAAAACCTACACACACCTCCTTGTTTTACTCTCTTT
CTCTCTCACACAACATGCACGCATACACACTTTTTGTGGTTTTTCACTTTTGATGCTTCA
TTTGGAATTTTTTTATGTTTAAGAATCATTCATCATGTAATAAATTTATTTTATTATTGG
GTATTGATTATGTTTAAAATTGAAATTTGTGGGATTTCATGCAAAAATGAATCGTAAGAT
TAGAAATTTAATTCTTCAAATAAAAAAATGAATAAAAATCATTATTATTATGAATATAAG
TAATTAAAT

>g8477.t2 Gene=g8477 Length=142
MMMRYLELLLLLLVVTTDAKIFTRCELAKELFNSGIPKTFISNWVCLIEAESGADTSKVT
EFPNLSASYGIFQINSKEWCRKSRKGGECGTRCEDFLTEDIKNDIRCAKVIYNRHGFSYW
KGWTSRCKSRPLPDVSKCFGRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g8477.t2 CDD cd16899 LYZ_C_invert 20 138 9.44927E-59
14 g8477.t2 Gene3D G3DSA:1.10.530.10 - 16 139 8.7E-44
2 g8477.t2 PANTHER PTHR11407 LYSOZYME C 6 139 2.5E-47
3 g8477.t2 PANTHER PTHR11407:SF63 LYSOZYME 6 139 2.5E-47
11 g8477.t2 PRINTS PR00137 Lysozyme signature 21 39 7.3E-5
7 g8477.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 7.4E-16
4 g8477.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 7.4E-16
6 g8477.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 66 82 7.4E-16
10 g8477.t2 PRINTS PR00137 Lysozyme signature 94 109 7.3E-5
8 g8477.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 97 112 7.4E-16
9 g8477.t2 PRINTS PR00137 Lysozyme signature 115 124 7.3E-5
5 g8477.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 116 127 7.4E-16
1 g8477.t2 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 138 1.4E-29
16 g8477.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
17 g8477.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
18 g8477.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 15 -
19 g8477.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 19 -
15 g8477.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 142 -
22 g8477.t2 ProSitePatterns PS00128 Glycosyl hydrolases family 22 (GH22) domain signature. 89 107 -
23 g8477.t2 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 141 31.439
21 g8477.t2 SMART SM00263 lysozyme-fin 20 139 1.4E-40
12 g8477.t2 SUPERFAMILY SSF53955 Lysozyme-like 19 139 6.97E-41
13 g8477.t2 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