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.t2 TSS g1249.t2 9121509 9121509
chr_3 g1249 g1249.t2 isoform g1249.t2 9121543 9122033
chr_3 g1249 g1249.t2 exon g1249.t2.exon1 9121543 9121783
chr_3 g1249 g1249.t2 cds g1249.t2.CDS1 9121543 9121783
chr_3 g1249 g1249.t2 exon g1249.t2.exon2 9121912 9122033
chr_3 g1249 g1249.t2 cds g1249.t2.CDS2 9121912 9122033
chr_3 g1249 g1249.t2 TTS g1249.t2 9122317 9122317

Sequences

>g1249.t2 Gene=g1249 Length=363
ATGAAAACTTTAATTTTTACAACTTTATTTGTTGCATTTTTCGCTTATACAAATGCGAAA
ATTTATTCAAAATGTGAACTTGTGGAAGAATTGCATAATGCTGGATTTCCGAAAGAAGAT
TTACCAGATTGGGTATGTTTAGTTGAGCATGAAAGTAATTATGATTCAGAAGCTATCGGT
GAAGAAAATCATGATGGATCTCAAGATTATGGCATTTTTCAAATCAATTCAAAATACTGG
TGTGATGACATTCAATGTGCAAAAATGATTTTTGATCGTCATCATTTTGATGCATGGTAT
GGTTGGATCAATAACTGCAAAGGTGCTGAGCTTCCTTCAATTGATGAATGCAATGTTAAA
TAG

>g1249.t2 Gene=g1249 Length=120
MKTLIFTTLFVAFFAYTNAKIYSKCELVEELHNAGFPKEDLPDWVCLVEHESNYDSEAIG
EENHDGSQDYGIFQINSKYWCDDIQCAKMIFDRHHFDAWYGWINNCKGAELPSIDECNVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g1249.t2 CDD cd16899 LYZ_C_invert 20 117 1.08282E-53
11 g1249.t2 Gene3D G3DSA:1.10.530.10 - 20 82 4.4E-29
12 g1249.t2 Gene3D G3DSA:1.10.530.10 - 83 119 2.7E-7
3 g1249.t2 PANTHER PTHR11407 LYSOZYME C 1 82 2.9E-39
5 g1249.t2 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 1 82 2.9E-39
2 g1249.t2 PANTHER PTHR11407 LYSOZYME C 82 118 2.9E-39
4 g1249.t2 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 82 118 2.9E-39
7 g1249.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 2.7E-9
6 g1249.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 2.7E-9
8 g1249.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 67 83 2.7E-9
1 g1249.t2 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 83 3.5E-19
14 g1249.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
15 g1249.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
16 g1249.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
17 g1249.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
13 g1249.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 120 -
20 g1249.t2 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 120 23.587
19 g1249.t2 SMART SM00263 lysozyme-fin 20 118 4.7E-37
9 g1249.t2 SUPERFAMILY SSF53955 Lysozyme-like 20 117 2.95E-35
10 g1249.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

There are no GO annotations for this transcript.

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