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.t3 isoform g2453.t3 18031734 18047135
chr_3 g2453 g2453.t3 exon g2453.t3.exon1 18031734 18032198
chr_3 g2453 g2453.t3 cds g2453.t3.CDS1 18031993 18032198
chr_3 g2453 g2453.t3 exon g2453.t3.exon2 18038878 18039019
chr_3 g2453 g2453.t3 cds g2453.t3.CDS2 18038878 18039019
chr_3 g2453 g2453.t3 exon g2453.t3.exon3 18039101 18039684
chr_3 g2453 g2453.t3 cds g2453.t3.CDS3 18039101 18039684
chr_3 g2453 g2453.t3 exon g2453.t3.exon4 18039768 18039975
chr_3 g2453 g2453.t3 cds g2453.t3.CDS4 18039768 18039975
chr_3 g2453 g2453.t3 exon g2453.t3.exon5 18040042 18040157
chr_3 g2453 g2453.t3 cds g2453.t3.CDS5 18040042 18040157
chr_3 g2453 g2453.t3 exon g2453.t3.exon6 18047123 18047135
chr_3 g2453 g2453.t3 cds g2453.t3.CDS6 18047123 18047135
chr_3 g2453 g2453.t3 TSS g2453.t3 18047308 18047308
chr_3 g2453 g2453.t3 TTS g2453.t3 NA NA

Sequences

>g2453.t3 Gene=g2453 Length=1528
ATGCTGCAAAAATTAATTCTCTCAGTTTGTGCTCTGACTATCGTGCTAAACGCATCAATG
GCGTCACCCTCTGAAATCGAACAAAAGTTTTCAAAATCAGCCAGCAACTTTGCTGCTAAA
TTGTACCAAAACTCAATTCAAGGAAAAACTGGCAATGTAATTATTTCACCTGTCTCAGTT
CAAACAGCCGTCACTTTGGCTATGTTTGGTGCTGCTGGTGAGACCAAGCAAGAAATGTTA
AAAGGTCTCGAATATCAGGGTTTCACTGATCAAATAATTGCTGATAACTATCAACGATTT
GGCGAGAGCGTCGCAAAGACTAATGGATTGAAAATCGCTAATAAGATTTATGTGATGAAA
GGCTATTCAGTCAAGCCAACATTCCAGCAAGTCGCAACAAAGAGTTTCAATTCAGAAGCT
GAAGATGTAAATTTCGCACAAAGTAAAGACTCAGCTGGCAAAATCAATACATGGGTTGAA
AATCAAACAAATAATAAAATTAAAAATCTTATCTCACCTGATTCATTGGATGCTGACACA
CGTATGGTTCTTGTAAATGCCATTTACTTCAAAGGATTCTGGACCTATCAATTTGATCCA
AAAGCAACATTCAAAGCACCATTCTTTCTCAATGATAATGATAAAGTTGATGTTGATTTC
ATGAAAATTAAGAAACATTTCAAATATGGACGATTTGATGATCTTGATGCAACTGCATTG
GAATTGCCTTACAAAGATTCTGATATTACAATGTTGATAATTTTACCAAATAAACGCACT
GGATTGGCTGAATTGGAGAGCAAATTGGACACAATTGACTTCAATGAGCTCACAACAAAG
ATGTATTCGGAAGAAGTTAATGTTGAATTGCCAAAGTTTAAAATTGAATTTGACATTGAA
TTGACCGAGCCATTAAAGAAGATGGGAATGGAGAAAATGTTCTCAGATGCTGCTCAATTT
GATGAATTGCTTACATCGACTGAACCTCTCAAGGTTTCACAAGTTGTTCATAAAGCCTTC
ATTGAAGTCAATGAAGAAGGTGCTGAAGCAGCTGCTGCTACAGAATTTTTCTTAGAATTT
CATATAAACGAAGACACCAAATTCATAGCAAGTCACCCTTTCCTCTTTAAAATTGTTCAA
AATGAAAAAGATTTATTCTTAGGAAGAGTAACAATGGAAATAAATTTGGAAAGGCATGCA
ATAATTCATTTTCCAGATGATTATAATAAATATCGTCACGATTGGGAAGGTCAGATTTTT
TATTTCTAAATATAAAAGTTGTTCATCTTAAATTTAGTTAGACTAATAAAATGACATATT
TCGTAGGAATAATACTTAAATTCTGCTGTTTTCATTTATTTCTCCTTCTTTTGATTTAAT
TTTGTTACCTGAATATCATGAAATTTTATTATTATACCTTCACCCTATATACAATTTATT
TTTCAGACACATCTACCTAAATTTCAATGCCAGTCACCCATGTTTACAGTTAATTCTTTC
GCGTTGCATTTTATATCTTAAATAATTT

>g2453.t3 Gene=g2453 Length=422
MLQKLILSVCALTIVLNASMASPSEIEQKFSKSASNFAAKLYQNSIQGKTGNVIISPVSV
QTAVTLAMFGAAGETKQEMLKGLEYQGFTDQIIADNYQRFGESVAKTNGLKIANKIYVMK
GYSVKPTFQQVATKSFNSEAEDVNFAQSKDSAGKINTWVENQTNNKIKNLISPDSLDADT
RMVLVNAIYFKGFWTYQFDPKATFKAPFFLNDNDKVDVDFMKIKKHFKYGRFDDLDATAL
ELPYKDSDITMLIILPNKRTGLAELESKLDTIDFNELTTKMYSEEVNVELPKFKIEFDIE
LTEPLKKMGMEKMFSDAAQFDELLTSTEPLKVSQVVHKAFIEVNEEGAEAAAATEFFLEF
HINEDTKFIASHPFLFKIVQNEKDLFLGRVTMEINLERHAIIHFPDDYNKYRHDWEGQIF
YF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2453.t3 CDD cd19601 serpin42Da-like 33 389 2.40163E-146
8 g2453.t3 Gene3D G3DSA:3.30.497.10 Antithrombin 39 361 4.9E-117
7 g2453.t3 Gene3D G3DSA:2.30.39.10 - 195 389 4.9E-117
2 g2453.t3 PANTHER PTHR11461 SERINE PROTEASE INHIBITOR, SERPIN 30 390 2.9E-90
3 g2453.t3 PANTHER PTHR11461:SF180 LEUKOCYTE ELASTASE INHIBITOR 30 390 2.9E-90
1 g2453.t3 Pfam PF00079 Serpin (serine protease inhibitor) 33 391 4.6E-111
10 g2453.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
11 g2453.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
12 g2453.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
13 g2453.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
9 g2453.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 422 -
16 g2453.t3 SMART SM00093 serpin2 39 393 2.0E-120
4 g2453.t3 SUPERFAMILY SSF56574 Serpins 21 391 3.01E-116
6 g2453.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
15 g2453.t3 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 20 -
5 g2453.t3 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