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 g1247 g1247.t3 TSS g1247.t3 9118955 9118955
chr_3 g1247 g1247.t3 isoform g1247.t3 9119015 9119486
chr_3 g1247 g1247.t3 exon g1247.t3.exon1 9119015 9119300
chr_3 g1247 g1247.t3 cds g1247.t3.CDS1 9119015 9119300
chr_3 g1247 g1247.t3 exon g1247.t3.exon2 9119358 9119486
chr_3 g1247 g1247.t3 cds g1247.t3.CDS2 9119358 9119485
chr_3 g1247 g1247.t3 TTS g1247.t3 NA NA

Sequences

>g1247.t3 Gene=g1247 Length=415
ATGAAATTTTTAATTGCTGCAATTTTATTTGTTGCAATTTTTGCTAATATTAACGCAAAA
ATTTATTCAAAATGTGAGCTCGTTCGAACACTTTATAATTCTGGTATTCCACAAAGTCAG
TTACGTGATTGGGCATGCTTAGTACAACATGAAAGTAGCTACAACTCAAAAGCAAAAGGA
GGACCAAACAAAAATGGCTCATATGACTATGGAATTTTTCAAATCAATTCAAAATATTGG
TGTGGAATTGGAAAAGTTGGTGGAGATTGTAATTTAAATTGCAATTCTTTGCTTACTGAT
GATATTAGTGATGACATTCGATGTGCAAAGATAATCTATAAACGTCATAATTTCAGTGCT
TGGTATGGTTGGGTTAATCATTGCAAAGGAAAAGCTCTGCCATCAATTTCAGAAT

>g1247.t3 Gene=g1247 Length=138
MKFLIAAILFVAIFANINAKIYSKCELVRTLYNSGIPQSQLRDWACLVQHESSYNSKAKG
GPNKNGSYDYGIFQINSKYWCGIGKVGGDCNLNCNSLLTDDISDDIRCAKIIYKRHNFSA
WYGWVNHCKGKALPSISE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g1247.t3 CDD cd16899 LYZ_C_invert 20 138 2.30178E-66
16 g1247.t3 Gene3D G3DSA:1.10.530.10 - 20 86 3.1E-27
17 g1247.t3 Gene3D G3DSA:1.10.530.10 - 88 138 1.3E-17
2 g1247.t3 PANTHER PTHR11407 LYSOZYME C 1 137 4.0E-51
3 g1247.t3 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 1 137 4.0E-51
13 g1247.t3 PRINTS PR00137 Lysozyme signature 21 39 3.2E-9
7 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 2.8E-20
6 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 2.8E-20
8 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 67 83 2.8E-20
5 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 88 97 2.8E-20
10 g1247.t3 PRINTS PR00137 Lysozyme signature 95 110 3.2E-9
4 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 98 113 2.8E-20
11 g1247.t3 PRINTS PR00137 Lysozyme signature 116 125 3.2E-9
9 g1247.t3 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 117 128 2.8E-20
12 g1247.t3 PRINTS PR00137 Lysozyme signature 126 138 3.2E-9
1 g1247.t3 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 135 6.1E-32
19 g1247.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
20 g1247.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
21 g1247.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
22 g1247.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
18 g1247.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 138 -
25 g1247.t3 ProSitePatterns PS00128 Glycosyl hydrolases family 22 (GH22) domain signature. 90 108 -
26 g1247.t3 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 138 37.31
24 g1247.t3 SMART SM00263 lysozyme-fin 20 138 3.7E-51
14 g1247.t3 SUPERFAMILY SSF53955 Lysozyme-like 19 136 1.26E-45
15 g1247.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 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