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.t1 TSS g5714.t1 11344235 11344235
chr_2 g5714 g5714.t1 isoform g5714.t1 11344268 11346015
chr_2 g5714 g5714.t1 exon g5714.t1.exon1 11344268 11344271
chr_2 g5714 g5714.t1 cds g5714.t1.CDS1 11344268 11344271
chr_2 g5714 g5714.t1 exon g5714.t1.exon2 11344331 11344413
chr_2 g5714 g5714.t1 cds g5714.t1.CDS2 11344331 11344413
chr_2 g5714 g5714.t1 exon g5714.t1.exon3 11344596 11344800
chr_2 g5714 g5714.t1 cds g5714.t1.CDS3 11344596 11344800
chr_2 g5714 g5714.t1 exon g5714.t1.exon4 11344860 11345273
chr_2 g5714 g5714.t1 cds g5714.t1.CDS4 11344860 11345273
chr_2 g5714 g5714.t1 exon g5714.t1.exon5 11345330 11346015
chr_2 g5714 g5714.t1 cds g5714.t1.CDS5 11345330 11346015
chr_2 g5714 g5714.t1 TTS g5714.t1 11346027 11346027

Sequences

>g5714.t1 Gene=g5714 Length=1392
ATGAGAGTTTTAAAATTCTTTTTAATATTATTGTGCATATTTTCCATAATTGTGCAAGTG
AAATGTGGACTCTTTAAGAAAGTTGGAAGCTTTTTAGGTGTCAAAAAAGAAAGTGATGAC
AGTGGTGAGGAAAATATAAATGCTCAAGTTGATACGGCTTATAAATTTGGTTCTTTAATC
ATTAAACCGGCTTTAAATTTACTACTTGGAAGTGATGATACAGATAGTTCAATAACTTCA
CAAAATCCTCAACGTCAAGATAAATTAGAGTCAACAACTCCATATAATTATGGAAACTAT
GCATTTTCACCAGGATATTATAAAGATTCACTCGTTCAATGTCCATCTGATGTGCTTAAA
GGTCAAACAATAACATTCACATGTTATAGAGAGAATTTTTTGATTCCATGTGATGATTAT
ATTTTTGCAAATGATACAGCTCAAATTAATTGTAAACCTGGTTATGAATATCCACAAGTT
AGTGGCATACAAACTAAAATTGAATGTAAACGAAATGGAAAATGGAGTGCACCTATTTTT
GAATGTGTTCCAAAATGTGGTCGTGTAACGAAAAAGGCTAAAGCTTTAGTGATTCATGGT
AGTGATACAGAAATATTAGAATTTCCATGGAATATTGCAATATATCATTCAAATATATTG
ATATGTAGTGGCAGCATTCTTTCAGAACGAATTGTATTATCAGCTGCTCATTGTTTCATG
AAAGAAACATCACATGGCATTGAACAATATCCATTAGAAAAGTATGAATTAATTGCTGGA
AAATATTTTCGTGATATTGATGCAATTGAAAGTCATCAAATTCAACGATTTAAAGTAGAA
AAAGTGAAAATTCATGATGCATATTATGGCTTCATAGGGAATTATGATGCTGATATTACA
ATTATAACTCTCGATAGATCTCTCGTTTATCAAACACATATTGCGCCTGTGTGTCTTAAT
TTAGAACTTAAAACACTTGCTGAAAAACAAGTTCCGCAACATGGAACTTTAGGAATTGTG
GCAGGTTATGGTTATACAGAAGCTGATGGAGCTCCAAGTGATCGTTTGAAAAAAATTGAA
CTGCCAATTGTTGATATAAAAGTCTGTAAGCAAGAAGCACCTGATAATTTCAAATCATTT
GTGACAAGTGATAAATTTTGTGCGGGATATAATGATGGATCAGGCGCAGTTTGTAAAGGT
GATAGTGGTGCAGGATTTACAACAGGAAAAATTATAGGTGATGAAACAATTTATTTTATT
CATGGTATTGTAAGCAATACTCGAGCAGTAAATGGTGGTTGTGATTTAAATTTTTATGCA
ATGTTTACTCATGTACAAAATTATGTTGACATGATTAAAGAAGAAATAAGACTTTCAAAA
ATTGATAAATAA

>g5714.t1 Gene=g5714 Length=463
MRVLKFFLILLCIFSIIVQVKCGLFKKVGSFLGVKKESDDSGEENINAQVDTAYKFGSLI
IKPALNLLLGSDDTDSSITSQNPQRQDKLESTTPYNYGNYAFSPGYYKDSLVQCPSDVLK
GQTITFTCYRENFLIPCDDYIFANDTAQINCKPGYEYPQVSGIQTKIECKRNGKWSAPIF
ECVPKCGRVTKKAKALVIHGSDTEILEFPWNIAIYHSNILICSGSILSERIVLSAAHCFM
KETSHGIEQYPLEKYELIAGKYFRDIDAIESHQIQRFKVEKVKIHDAYYGFIGNYDADIT
IITLDRSLVYQTHIAPVCLNLELKTLAEKQVPQHGTLGIVAGYGYTEADGAPSDRLKKIE
LPIVDIKVCKQEAPDNFKSFVTSDKFCAGYNDGSGAVCKGDSGAGFTTGKIIGDETIYFI
HGIVSNTRAVNGGCDLNFYAMFTHVQNYVDMIKEEIRLSKIDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5714.t1 CDD cd00033 CCP 125 183 5.68817E-4
20 g5714.t1 CDD cd00190 Tryp_SPc 197 454 3.73731E-50
11 g5714.t1 Gene3D G3DSA:2.10.70.10 Complement Module 129 184 5.3E-6
13 g5714.t1 Gene3D G3DSA:2.40.10.10 - 197 444 5.6E-49
12 g5714.t1 Gene3D G3DSA:2.40.10.10 - 209 452 5.6E-49
3 g5714.t1 PANTHER PTHR24260 - 132 456 2.0E-61
4 g5714.t1 PANTHER PTHR24260:SF129 MODULAR SERINE PROTEASE 132 456 2.0E-61
7 g5714.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 223 238 6.1E-6
6 g5714.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 294 308 6.1E-6
5 g5714.t1 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 395 407 6.1E-6
2 g5714.t1 Pfam PF00084 Sushi repeat (SCR repeat) 139 182 2.2E-4
1 g5714.t1 Pfam PF00089 Trypsin 198 452 2.4E-36
15 g5714.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
16 g5714.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
17 g5714.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
18 g5714.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
14 g5714.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 463 -
22 g5714.t1 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 233 238 -
23 g5714.t1 ProSiteProfiles PS50923 Sushi/CCP/SCR domain profile. 126 184 7.598
24 g5714.t1 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 197 457 24.051
21 g5714.t1 SMART SM00020 trypsin_2 196 452 7.4E-42
8 g5714.t1 SUPERFAMILY SSF57535 Complement control module/SCR domain 136 187 5.0E-6
9 g5714.t1 SUPERFAMILY SSF50494 Trypsin-like serine proteases 170 456 3.39E-55
10 g5714.t1 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5714.t1.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