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 g1248 g1248.t1 TSS g1248.t1 9120697 9120697
chr_3 g1248 g1248.t1 isoform g1248.t1 9120736 9121220
chr_3 g1248 g1248.t1 exon g1248.t1.exon1 9120736 9121021
chr_3 g1248 g1248.t1 cds g1248.t1.CDS1 9120736 9121021
chr_3 g1248 g1248.t1 exon g1248.t1.exon2 9121081 9121220
chr_3 g1248 g1248.t1 cds g1248.t1.CDS2 9121081 9121220
chr_3 g1248 g1248.t1 TTS g1248.t1 9121369 9121369

Sequences

>g1248.t1 Gene=g1248 Length=426
ATGAAAATTTTTATTATATCATTTTTGCTTTTTGCAATATTTGCATTTTCTGAAGCAAAA
GTTTTCACAAAATGTGAATTAGTCAAGGCACTTTATAAAGCTGGCATACCAAAATCAAAG
CTACGTGATTGGGCTTGTTTAGTACAACATGAAAGTAGCTACAACTCAAAAGCAAAAGGA
GGACCGAACAAAAATGGCTCATATGACTATGGGATTTTTCAAATCAATTCAAAATATTGG
TGTGGAATTGGAAAAGTTGGTGGAGATTGCAAAATAAATTGCAATTCATTAATTAATAAT
GACATCACTGATGACATCAAATGTGCTAAAACTATCTATAATCGACATAATTTTACAGCA
TGGTATGGCTGGAACAGTAAATGCAAAGAAAAGAAACTTCCTTCAATCAGTGAATGCACA
CTTTAA

>g1248.t1 Gene=g1248 Length=141
MKIFIISFLLFAIFAFSEAKVFTKCELVKALYKAGIPKSKLRDWACLVQHESSYNSKAKG
GPNKNGSYDYGIFQINSKYWCGIGKVGGDCKINCNSLINNDITDDIKCAKTIYNRHNFTA
WYGWNSKCKEKKLPSISECTL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g1248.t1 CDD cd16899 LYZ_C_invert 20 139 2.1747E-65
15 g1248.t1 Gene3D G3DSA:1.10.530.10 - 20 86 9.7E-27
16 g1248.t1 Gene3D G3DSA:1.10.530.10 - 88 141 2.9E-17
2 g1248.t1 PANTHER PTHR11407 LYSOZYME C 1 139 3.7E-49
3 g1248.t1 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 1 139 3.7E-49
12 g1248.t1 PRINTS PR00137 Lysozyme signature 21 39 3.9E-7
7 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 2.0E-19
6 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 2.0E-19
8 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 67 83 2.0E-19
5 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 88 97 2.0E-19
10 g1248.t1 PRINTS PR00137 Lysozyme signature 95 110 3.9E-7
4 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 98 113 2.0E-19
11 g1248.t1 PRINTS PR00137 Lysozyme signature 116 125 3.9E-7
9 g1248.t1 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 117 128 2.0E-19
1 g1248.t1 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 139 5.9E-32
18 g1248.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
19 g1248.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
20 g1248.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
21 g1248.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
17 g1248.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 141 -
25 g1248.t1 ProSitePatterns PS00128 Glycosyl hydrolases family 22 (GH22) domain signature. 90 108 -
26 g1248.t1 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 141 37.407
24 g1248.t1 SMART SM00263 lysozyme-fin 20 140 4.6E-51
13 g1248.t1 SUPERFAMILY SSF53955 Lysozyme-like 20 135 1.64E-45
14 g1248.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
23 g1248.t1 SignalP_GRAM_NEGATIVE 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

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