Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine protease inhibitor 42Dd.

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 g2453 g2453.t24 TTS g2453.t24 18033055 18033055
chr_3 g2453 g2453.t24 isoform g2453.t24 18033128 18047135
chr_3 g2453 g2453.t24 exon g2453.t24.exon1 18033128 18033263
chr_3 g2453 g2453.t24 cds g2453.t24.CDS1 18033139 18033263
chr_3 g2453 g2453.t24 exon g2453.t24.exon2 18038878 18039019
chr_3 g2453 g2453.t24 cds g2453.t24.CDS2 18038878 18039019
chr_3 g2453 g2453.t24 exon g2453.t24.exon3 18039101 18039684
chr_3 g2453 g2453.t24 cds g2453.t24.CDS3 18039101 18039684
chr_3 g2453 g2453.t24 exon g2453.t24.exon4 18039768 18039975
chr_3 g2453 g2453.t24 cds g2453.t24.CDS4 18039768 18039975
chr_3 g2453 g2453.t24 exon g2453.t24.exon5 18040042 18040157
chr_3 g2453 g2453.t24 cds g2453.t24.CDS5 18040042 18040157
chr_3 g2453 g2453.t24 exon g2453.t24.exon6 18047123 18047135
chr_3 g2453 g2453.t24 cds g2453.t24.CDS6 18047123 18047135
chr_3 g2453 g2453.t24 TSS g2453.t24 18047308 18047308

Sequences

>g2453.t24 Gene=g2453 Length=1199
ATGCTGCAAAAATTAATTCTCTCAGTTTGTGCTCTGACTATCGTGCTAAACGCATCAATG
GCGTCACCCTCTGAAATCGAACAAAAGTTTTCAAAATCAGCCAGCAACTTTGCTGCTAAA
TTGTACCAAAACTCAATTCAAGGAAAAACTGGCAATGTAATTATTTCACCTGTCTCAGTT
CAAACAGCCGTCACTTTGGCTATGTTTGGTGCTGCTGGTGAGACCAAGCAAGAAATGTTA
AAAGGTCTCGAATATCAGGGTTTCACTGATCAAATAATTGCTGATAACTATCAACGATTT
GGCGAGAGCGTCGCAAAGACTAATGGATTGAAAATCGCTAATAAGATTTATGTGATGAAA
GGCTATTCAGTCAAGCCAACATTCCAGCAAGTCGCAACAAAGAGTTTCAATTCAGAAGCT
GAAGATGTAAATTTCGCACAAAGTAAAGACTCAGCTGGCAAAATCAATACATGGGTTGAA
AATCAAACAAATAATAAAATTAAAAATCTTATCTCACCTGATTCATTGGATGCTGACACA
CGTATGGTTCTTGTAAATGCCATTTACTTCAAAGGATTCTGGACCTATCAATTTGATCCA
AAAGCAACATTCAAAGCACCATTCTTTCTCAATGATAATGATAAAGTTGATGTTGATTTC
ATGAAAATTAAGAAACATTTCAAATATGGACGATTTGATGATCTTGATGCAACTGCATTG
GAATTGCCTTACAAAGATTCTGATATTACAATGTTGATAATTTTACCAAATAAACGCACT
GGATTGGCTGAATTGGAGAGCAAATTGGACACAATTGACTTCAATGAGCTCACAACAAAG
ATGTATTCGGAAGAAGTTAATGTTGAATTGCCAAAGTTTAAAATTGAATTTGACATTGAA
TTGACCGAGCCATTAAAGAAGATGGGAATGGAGAAAATGTTCTCAGATGCTGCTCAATTT
GATGAATTGCTTACATCGACTGAACCTCTCAAGGTTTCACAAGTTGTTCATAAAGCCTTC
ATTGAAGTCAATGAAGAAGGTGCTGAAGCAGCTGCTGCTACAGCCCTTGAAATATCGGAT
CGCATCGCACTATTTTTTGATTGGAAATTTAAAGCAAATCACGCATTTTTCTTTGTTTTC
AAACAAGGCCAGCAATCATTGTTTTTGGGAAGAATCTCACAATTATGATGACAAAAAAA

>g2453.t24 Gene=g2453 Length=395
MLQKLILSVCALTIVLNASMASPSEIEQKFSKSASNFAAKLYQNSIQGKTGNVIISPVSV
QTAVTLAMFGAAGETKQEMLKGLEYQGFTDQIIADNYQRFGESVAKTNGLKIANKIYVMK
GYSVKPTFQQVATKSFNSEAEDVNFAQSKDSAGKINTWVENQTNNKIKNLISPDSLDADT
RMVLVNAIYFKGFWTYQFDPKATFKAPFFLNDNDKVDVDFMKIKKHFKYGRFDDLDATAL
ELPYKDSDITMLIILPNKRTGLAELESKLDTIDFNELTTKMYSEEVNVELPKFKIEFDIE
LTEPLKKMGMEKMFSDAAQFDELLTSTEPLKVSQVVHKAFIEVNEEGAEAAAATALEISD
RIALFFDWKFKANHAFFFVFKQGQQSLFLGRISQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2453.t24 CDD cd19601 serpin42Da-like 33 391 1.08195E-145
8 g2453.t24 Gene3D G3DSA:3.30.497.10 Antithrombin 49 340 2.8E-117
7 g2453.t24 Gene3D G3DSA:2.30.39.10 - 190 390 2.8E-117
2 g2453.t24 PANTHER PTHR11461 SERINE PROTEASE INHIBITOR, SERPIN 30 393 3.8E-89
3 g2453.t24 PANTHER PTHR11461:SF180 LEUKOCYTE ELASTASE INHIBITOR 30 393 3.8E-89
1 g2453.t24 Pfam PF00079 Serpin (serine protease inhibitor) 33 393 1.1E-108
10 g2453.t24 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
11 g2453.t24 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
12 g2453.t24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
13 g2453.t24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
9 g2453.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 395 -
16 g2453.t24 SMART SM00093 serpin2 39 395 1.9E-119
4 g2453.t24 SUPERFAMILY SSF56574 Serpins 21 393 2.49E-117
6 g2453.t24 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
15 g2453.t24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 20 -
5 g2453.t24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 21 -

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:0005615 extracellular space CC
GO:0004867 serine-type endopeptidase inhibitor activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following 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.

Raw TPM values