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.t6 isoform g8477.t6 30885833 30887780
chr_2 g8477 g8477.t6 exon g8477.t6.exon1 30885833 30886139
chr_2 g8477 g8477.t6 TSS g8477.t6 30885878 30885878
chr_2 g8477 g8477.t6 exon g8477.t6.exon2 30886508 30886656
chr_2 g8477 g8477.t6 cds g8477.t6.CDS1 30886527 30886656
chr_2 g8477 g8477.t6 exon g8477.t6.exon3 30886745 30886897
chr_2 g8477 g8477.t6 cds g8477.t6.CDS2 30886745 30886897
chr_2 g8477 g8477.t6 exon g8477.t6.exon4 30886995 30887075
chr_2 g8477 g8477.t6 cds g8477.t6.CDS3 30886995 30887075
chr_2 g8477 g8477.t6 exon g8477.t6.exon5 30887140 30887191
chr_2 g8477 g8477.t6 cds g8477.t6.CDS4 30887140 30887191
chr_2 g8477 g8477.t6 exon g8477.t6.exon6 30887466 30887780
chr_2 g8477 g8477.t6 cds g8477.t6.CDS5 30887466 30887613
chr_2 g8477 g8477.t6 TTS g8477.t6 30887790 30887790

Sequences

>g8477.t6 Gene=g8477 Length=1057
AAAAATACAATTTAAGTAGAGTGATAGTCATAGCATGCGAGTTCTCAGTTTGTGTTCATC
GTCTTTAGAGTCAAATAGCTAAGAGTAATCGCGTTATAAATTTGTTTTCATTAAAAGATT
TACTTGCGAAAATTTCATCAATAAATAATCAAAAATATTATTTGGGTGTTAAAATCTTTA
ATCCACTAAACAATTCAATTAAGCCTGATCTTTTATAGAAAGGAAAAAAGGTGTTAATTG
ATCTTTTATGAATCAATTGAAAGTGATTCCTTTCATGAATAACTGGAGTGAAAATCTTAC
TCATTCGTCTACTTAGAAAATCAACGATGATGATGAGGTACCTGGAGTTGTTATTATTAT
TGCTAGTTGTTACAACAGATGCCAAAATATTCACAAGATGTGAATTAGCAAAGGAACTTT
TCAATAGTGGCATTCCAAAGACATTCATCTCAAATTGGGTTTGCTTGATCGAGGCAGAAT
CAGGTGCTGACACATCAAAAGTTACAGAATTTCCGAATCTAAGTGCCAGTTATGGGATAT
TTCAGATAAACTCAAAAGAATGGTGCCGTAAATCGCGAAAAGGAGGCGAGTGTGGGACGC
GTTGTGAAGACTTTTTAACTGAAGATATTAAAAATGATATAAGATGCGCTAAAGTCATAT
ACAATCGTCATGGATTTTCATATTGGAAAGGTTGGACATCACGATGCAAATCTCGTCCAT
TACCTGATGTGTCAAAATGTTCGCTTTGGCAGAAAGTAAGAAAAATGCAAATAAAAACCT
ACACACACCTCCTTGTTTTACTCTCTTTCTCTCTCACACAACATGCACGCATACACACTT
TTTGTGGTTTTTCACTTTTGATGCTTCATTTGGAATTTTTTTATGTTTAAGAATCATTCA
TCATGTAATAAATTTATTTTATTATTGGGTATTGATTATGTTTAAAATTGAAATTTGTGG
GATTTCATGCAAAAATGAATCGTAAGATTAGAAATTTAATTCTTCAAATAAAAAAATGAA
TAAAAATCATTATTATTATGAATATAAGTAATTAAAT

>g8477.t6 Gene=g8477 Length=187
MMMRYLELLLLLLVVTTDAKIFTRCELAKELFNSGIPKTFISNWVCLIEAESGADTSKVT
EFPNLSASYGIFQINSKEWCRKSRKGGECGTRCEDFLTEDIKNDIRCAKVIYNRHGFSYW
KGWTSRCKSRPLPDVSKCSLWQKVRKMQIKTYTHLLVLLSFSLTQHARIHTFCGFSLLML
HLEFFYV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g8477.t6 CDD cd16899 LYZ_C_invert 20 138 1.65749E-60
11 g8477.t6 Gene3D G3DSA:1.10.530.10 - 16 151 2.4E-42
2 g8477.t6 PANTHER PTHR11407 LYSOZYME C 6 147 1.6E-47
3 g8477.t6 PANTHER PTHR11407:SF63 LYSOZYME 6 147 1.6E-47
7 g8477.t6 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 1.9E-15
4 g8477.t6 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 1.9E-15
6 g8477.t6 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 66 82 1.9E-15
8 g8477.t6 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 97 112 1.9E-15
5 g8477.t6 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 116 127 1.9E-15
1 g8477.t6 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 138 5.3E-29
13 g8477.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
14 g8477.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
15 g8477.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 15 -
16 g8477.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 19 -
12 g8477.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 187 -
19 g8477.t6 ProSitePatterns PS00128 Glycosyl hydrolases family 22 (GH22) domain signature. 89 107 -
20 g8477.t6 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 141 32.086
18 g8477.t6 SMART SM00263 lysozyme-fin 20 139 6.0E-40
9 g8477.t6 SUPERFAMILY SSF53955 Lysozyme-like 19 138 4.29E-40
10 g8477.t6 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

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