Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Limulus clotting factor C.

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 g5714 g5714.t4 TSS g5714.t4 11344235 11344235
chr_2 g5714 g5714.t4 isoform g5714.t4 11344268 11346015
chr_2 g5714 g5714.t4 exon g5714.t4.exon1 11344268 11344271
chr_2 g5714 g5714.t4 cds g5714.t4.CDS1 11344268 11344271
chr_2 g5714 g5714.t4 exon g5714.t4.exon2 11344331 11344413
chr_2 g5714 g5714.t4 cds g5714.t4.CDS2 11344331 11344413
chr_2 g5714 g5714.t4 exon g5714.t4.exon3 11344596 11344800
chr_2 g5714 g5714.t4 cds g5714.t4.CDS3 11344596 11344800
chr_2 g5714 g5714.t4 exon g5714.t4.exon4 11344881 11345273
chr_2 g5714 g5714.t4 cds g5714.t4.CDS4 11344881 11345273
chr_2 g5714 g5714.t4 exon g5714.t4.exon5 11345330 11346015
chr_2 g5714 g5714.t4 cds g5714.t4.CDS5 11345330 11346015
chr_2 g5714 g5714.t4 TTS g5714.t4 11346027 11346027

Sequences

>g5714.t4 Gene=g5714 Length=1371
ATGAGAGTTTTAAAATTCTTTTTAATATTATTGTGCATATTTTCCATAATTGTGCAAGTG
AAATGTGGACTCTTTAAGAAAGTTGGAAGCTTTTTAGGTGTCAAAAAAGAAAGTGATGAC
AGTGGTGAGGAAAATATAAATGCTCAAGTTGATACGGCTTATAAATTTGGTTCTTTAATC
ATTAAACCGGCTTTAAATTTACTACTTGGAAGTGATGATACAGATAGTTCAATAACTTCA
CAAAATCCTCAACGTCAAGATAAATTAGAGTCAACAACTCCATATAATTATGGATATTAT
AAAGATTCACTCGTTCAATGTCCATCTGATGTGCTTAAAGGTCAAACAATAACATTCACA
TGTTATAGAGAGAATTTTTTGATTCCATGTGATGATTATATTTTTGCAAATGATACAGCT
CAAATTAATTGTAAACCTGGTTATGAATATCCACAAGTTAGTGGCATACAAACTAAAATT
GAATGTAAACGAAATGGAAAATGGAGTGCACCTATTTTTGAATGTGTTCCAAAATGTGGT
CGTGTAACGAAAAAGGCTAAAGCTTTAGTGATTCATGGTAGTGATACAGAAATATTAGAA
TTTCCATGGAATATTGCAATATATCATTCAAATATATTGATATGTAGTGGCAGCATTCTT
TCAGAACGAATTGTATTATCAGCTGCTCATTGTTTCATGAAAGAAACATCACATGGCATT
GAACAATATCCATTAGAAAAGTATGAATTAATTGCTGGAAAATATTTTCGTGATATTGAT
GCAATTGAAAGTCATCAAATTCAACGATTTAAAGTAGAAAAAGTGAAAATTCATGATGCA
TATTATGGCTTCATAGGGAATTATGATGCTGATATTACAATTATAACTCTCGATAGATCT
CTCGTTTATCAAACACATATTGCGCCTGTGTGTCTTAATTTAGAACTTAAAACACTTGCT
GAAAAACAAGTTCCGCAACATGGAACTTTAGGAATTGTGGCAGGTTATGGTTATACAGAA
GCTGATGGAGCTCCAAGTGATCGTTTGAAAAAAATTGAACTGCCAATTGTTGATATAAAA
GTCTGTAAGCAAGAAGCACCTGATAATTTCAAATCATTTGTGACAAGTGATAAATTTTGT
GCGGGATATAATGATGGATCAGGCGCAGTTTGTAAAGGTGATAGTGGTGCAGGATTTACA
ACAGGAAAAATTATAGGTGATGAAACAATTTATTTTATTCATGGTATTGTAAGCAATACT
CGAGCAGTAAATGGTGGTTGTGATTTAAATTTTTATGCAATGTTTACTCATGTACAAAAT
TATGTTGACATGATTAAAGAAGAAATAAGACTTTCAAAAATTGATAAATAA

>g5714.t4 Gene=g5714 Length=456
MRVLKFFLILLCIFSIIVQVKCGLFKKVGSFLGVKKESDDSGEENINAQVDTAYKFGSLI
IKPALNLLLGSDDTDSSITSQNPQRQDKLESTTPYNYGYYKDSLVQCPSDVLKGQTITFT
CYRENFLIPCDDYIFANDTAQINCKPGYEYPQVSGIQTKIECKRNGKWSAPIFECVPKCG
RVTKKAKALVIHGSDTEILEFPWNIAIYHSNILICSGSILSERIVLSAAHCFMKETSHGI
EQYPLEKYELIAGKYFRDIDAIESHQIQRFKVEKVKIHDAYYGFIGNYDADITIITLDRS
LVYQTHIAPVCLNLELKTLAEKQVPQHGTLGIVAGYGYTEADGAPSDRLKKIELPIVDIK
VCKQEAPDNFKSFVTSDKFCAGYNDGSGAVCKGDSGAGFTTGKIIGDETIYFIHGIVSNT
RAVNGGCDLNFYAMFTHVQNYVDMIKEEIRLSKIDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5714.t4 CDD cd00033 CCP 118 176 5.38311E-4
20 g5714.t4 CDD cd00190 Tryp_SPc 190 447 3.1819E-50
11 g5714.t4 Gene3D G3DSA:2.10.70.10 Complement Module 122 177 5.5E-6
13 g5714.t4 Gene3D G3DSA:2.40.10.10 - 190 437 5.4E-49
12 g5714.t4 Gene3D G3DSA:2.40.10.10 - 202 445 5.4E-49
3 g5714.t4 PANTHER PTHR24260 - 126 449 2.4E-61
4 g5714.t4 PANTHER PTHR24260:SF129 MODULAR SERINE PROTEASE 126 449 2.4E-61
5 g5714.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 216 231 5.9E-6
7 g5714.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 287 301 5.9E-6
6 g5714.t4 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 388 400 5.9E-6
2 g5714.t4 Pfam PF00084 Sushi repeat (SCR repeat) 132 175 3.1E-4
1 g5714.t4 Pfam PF00089 Trypsin 191 445 2.3E-36
15 g5714.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
16 g5714.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
17 g5714.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
18 g5714.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
14 g5714.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 456 -
22 g5714.t4 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 226 231 -
23 g5714.t4 ProSiteProfiles PS50923 Sushi/CCP/SCR domain profile. 119 177 7.598
24 g5714.t4 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 190 450 24.051
21 g5714.t4 SMART SM00020 trypsin_2 189 445 7.4E-42
8 g5714.t4 SUPERFAMILY SSF57535 Complement control module/SCR domain 124 180 6.25E-6
9 g5714.t4 SUPERFAMILY SSF50494 Trypsin-like serine proteases 163 449 3.23E-55
10 g5714.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5714/g5714.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5714.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004252 serine-type endopeptidase activity MF
GO:0006508 proteolysis BP

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.

Raw TPM values