Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Brachyurin.

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_4 g16394 g16394.t11 TSS g16394.t11 9323582 9323582
chr_4 g16394 g16394.t11 isoform g16394.t11 9323612 9324864
chr_4 g16394 g16394.t11 exon g16394.t11.exon1 9323612 9324054
chr_4 g16394 g16394.t11 cds g16394.t11.CDS1 9323612 9324054
chr_4 g16394 g16394.t11 exon g16394.t11.exon2 9324359 9324439
chr_4 g16394 g16394.t11 cds g16394.t11.CDS2 9324359 9324439
chr_4 g16394 g16394.t11 exon g16394.t11.exon3 9324494 9324637
chr_4 g16394 g16394.t11 cds g16394.t11.CDS3 9324494 9324637
chr_4 g16394 g16394.t11 exon g16394.t11.exon4 9324699 9324864
chr_4 g16394 g16394.t11 cds g16394.t11.CDS4 9324699 9324864
chr_4 g16394 g16394.t11 TTS g16394.t11 9324913 9324913

Sequences

>g16394.t11 Gene=g16394 Length=834
ATGAAGTTCTTTCTTTTAACAATTTTTGCAATCGCTGTTGTGTCAGCAGTTGAAGATTAT
AATGCACCAGAATGGCAACCAATTGATTGGGCAAAAGTAATTCCTGCTGATGAGTTGCCA
GGTTTCTGGGAAAATACAGTTTTCGCTCAACTTGCACCAAGATCAAACAGAGAGCGCAGA
ATTGTTGGTGGTCATGAAGCAACACCACATGCTCATCCATATCAAGTCGCTCTGATTCAT
CAACGTGTAATCTTGGCTACAATGTGTGGTGGTTCAGTTATTAGTCCAACTGTTATTCTC
ACAGCTGCTCATTGTCCAATTGGTTCACAATCATCAACTGTCATCACTGGAGCACATAAT
ATGAATGTAATTGAACCAAATCAACAACGTAGAACTGTTCAATCAGCACAATATCGTATT
CATGCTAATTATAATTCACAAAATTTGAATAACGATATCGCTACCATGATCCTTTTGCAA
CCATTGACACTCAACCAATTTGTTGCTGTTATTCCATTGGCACAAACAGTTGATGGTGGT
GCTTCGTCACCAGTTTTGCGAGTTGTTCAAAATCCAATTATCACAAATGCTGTTTGTGCA
CAAACCTTTGGAACTGCTGTTGTAAATGCAGCTGTTATATGCACTGATACTACTGGTGGA
CGTGGAACATGTCAAGGTGATTCGGGTGGAGTTCTTTCAGTATCGCAAGGTTCAGGACGT
CTTCAAGTTGGTATTACGAGTTTTGGCAGCAGTGCAGGATGTCAAGCAGGCTTTCCAGCT
GGCTATGAAAGAGTGAGTGCACAAATCGGATGGATTAACAGCAATATGTCATAA

>g16394.t11 Gene=g16394 Length=277
MKFFLLTIFAIAVVSAVEDYNAPEWQPIDWAKVIPADELPGFWENTVFAQLAPRSNRERR
IVGGHEATPHAHPYQVALIHQRVILATMCGGSVISPTVILTAAHCPIGSQSSTVITGAHN
MNVIEPNQQRRTVQSAQYRIHANYNSQNLNNDIATMILLQPLTLNQFVAVIPLAQTVDGG
ASSPVLRVVQNPIITNAVCAQTFGTAVVNAAVICTDTTGGRGTCQGDSGGVLSVSQGSGR
LQVGITSFGSSAGCQAGFPAGYERVSAQIGWINSNMS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g16394.t11 CDD cd00190 Tryp_SPc 61 275 3.71287E-61
11 g16394.t11 Gene3D G3DSA:2.40.10.10 - 61 106 1.2E-14
13 g16394.t11 Gene3D G3DSA:2.40.10.10 - 111 183 8.4E-12
12 g16394.t11 Gene3D G3DSA:2.40.10.10 - 184 277 7.3E-20
2 g16394.t11 PANTHER PTHR24250:SF56 SERINE PROTEASE P96 9 175 6.6E-68
4 g16394.t11 PANTHER PTHR24250 CHYMOTRYPSIN-RELATED 9 175 6.6E-68
3 g16394.t11 PANTHER PTHR24250:SF56 SERINE PROTEASE P96 180 274 6.6E-68
5 g16394.t11 PANTHER PTHR24250 CHYMOTRYPSIN-RELATED 180 274 6.6E-68
7 g16394.t11 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 90 105 3.5E-10
6 g16394.t11 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 148 162 3.5E-10
8 g16394.t11 PRINTS PR00722 Chymotrypsin serine protease family (S1) signature 221 233 3.5E-10
1 g16394.t11 Pfam PF00089 Trypsin 61 272 1.2E-38
15 g16394.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
16 g16394.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
17 g16394.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
18 g16394.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
14 g16394.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 277 -
21 g16394.t11 ProSitePatterns PS00134 Serine proteases, trypsin family, histidine active site. 100 105 -
22 g16394.t11 ProSitePatterns PS00135 Serine proteases, trypsin family, serine active site. 222 233 -
23 g16394.t11 ProSiteProfiles PS50240 Serine proteases, trypsin domain profile. 61 277 24.469
20 g16394.t11 SMART SM00020 trypsin_2 60 272 3.2E-55
9 g16394.t11 SUPERFAMILY SSF50494 Trypsin-like serine proteases 53 276 8.84E-57
10 g16394.t11 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

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: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. There were no conditions that were differentially expressed