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.t114 TTS g2453.t114 18036404 18036404
chr_3 g2453 g2453.t114 isoform g2453.t114 18036409 18042146
chr_3 g2453 g2453.t114 exon g2453.t114.exon1 18036409 18036585
chr_3 g2453 g2453.t114 cds g2453.t114.CDS1 18036455 18036585
chr_3 g2453 g2453.t114 exon g2453.t114.exon2 18038878 18039019
chr_3 g2453 g2453.t114 cds g2453.t114.CDS2 18038878 18039019
chr_3 g2453 g2453.t114 exon g2453.t114.exon3 18039101 18039684
chr_3 g2453 g2453.t114 cds g2453.t114.CDS3 18039101 18039684
chr_3 g2453 g2453.t114 exon g2453.t114.exon4 18039768 18039975
chr_3 g2453 g2453.t114 cds g2453.t114.CDS4 18039768 18039975
chr_3 g2453 g2453.t114 exon g2453.t114.exon5 18040042 18040157
chr_3 g2453 g2453.t114 cds g2453.t114.CDS5 18040042 18040157
chr_3 g2453 g2453.t114 exon g2453.t114.exon6 18041800 18042146
chr_3 g2453 g2453.t114 cds g2453.t114.CDS6 18041800 18041830
chr_3 g2453 g2453.t114 TSS g2453.t114 18042146 18042146

Sequences

>g2453.t114 Gene=g2453 Length=1574
GTTTGAAATCGTTCATTGAGAAAAGAACACGTGAAAAAAAAATAATTTAGTCACAAATCA
GTAAAATTGTTGTGATAAATTTTCCATTAATTTCCTAGTTTTTTTAAGTTAATATTTACA
AAGGCCATTATGTCAAATAAAAAATTTAATGTCACAAACTAATTGAATTTTAGCTACTGA
TGGTTTTTATGATTATTAGTGTGAAAAATACCAAATACGAGCCAAATAATATTATTGAAC
TTGAGTGAGCTTATATAAACATATATTGTCGTCATTAACATTTACTGTTTAGAAAAAAAT
TACTGAAATCAGAAATATGATTTTATCAAAACTTGTTAATAAAACATTAATTCTCTCAGT
TTGTGCTCTGACTATCGTGCTAAACGCATCAATGGCGTCACCCTCTGAAATCGAACAAAA
GTTTTCAAAATCAGCCAGCAACTTTGCTGCTAAATTGTACCAAAACTCAATTCAAGGAAA
AACTGGCAATGTAATTATTTCACCTGTCTCAGTTCAAACAGCCGTCACTTTGGCTATGTT
TGGTGCTGCTGGTGAGACCAAGCAAGAAATGTTAAAAGGTCTCGAATATCAGGGTTTCAC
TGATCAAATAATTGCTGATAACTATCAACGATTTGGCGAGAGCGTCGCAAAGACTAATGG
ATTGAAAATCGCTAATAAGATTTATGTGATGAAAGGCTATTCAGTCAAGCCAACATTCCA
GCAAGTCGCAACAAAGAGTTTCAATTCAGAAGCTGAAGATGTAAATTTCGCACAAAGTAA
AGACTCAGCTGGCAAAATCAATACATGGGTTGAAAATCAAACAAATAATAAAATTAAAAA
TCTTATCTCACCTGATTCATTGGATGCTGACACACGTATGGTTCTTGTAAATGCCATTTA
CTTCAAAGGATTCTGGACCTATCAATTTGATCCAAAAGCAACATTCAAAGCACCATTCTT
TCTCAATGATAATGATAAAGTTGATGTTGATTTCATGAAAATTAAGAAACATTTCAAATA
TGGACGATTTGATGATCTTGATGCAACTGCATTGGAATTGCCTTACAAAGATTCTGATAT
TACAATGTTGATAATTTTACCAAATAAACGCACTGGATTGGCTGAATTGGAGAGCAAATT
GGACACAATTGACTTCAATGAGCTCACAACAAAGATGTATTCGGAAGAAGTTAATGTTGA
ATTGCCAAAGTTTAAAATTGAATTTGACATTGAATTGACCGAGCCATTAAAGAAGATGGG
AATGGAGAAAATGTTCTCAGATGCTGCTCAATTTGATGAATTGCTTACATCGACTGAACC
TCTCAAGGTTTCACAAGTTGTTCATAAAGCCTTCATTGAAGTCAATGAAGAAGGTGCTGA
AGCAGCTGCTGCTACAGCAATGATTATGATGTCAAGATGTGCAATGATTTCTCGTTCTCA
ACAATTTATTGCGAACCGTCCATTTATTTTTGCATTGAAATTTGTTGCAGATGCTTTGTT
TGTTGGAAGAATCGAAAATTTTAATTGAAATAAAGTATTACATGCTTGAATTCAATAAAA
ATTGTAATGAAAAT

>g2453.t114 Gene=g2453 Length=403
MILSKLVNKTLILSVCALTIVLNASMASPSEIEQKFSKSASNFAAKLYQNSIQGKTGNVI
ISPVSVQTAVTLAMFGAAGETKQEMLKGLEYQGFTDQIIADNYQRFGESVAKTNGLKIAN
KIYVMKGYSVKPTFQQVATKSFNSEAEDVNFAQSKDSAGKINTWVENQTNNKIKNLISPD
SLDADTRMVLVNAIYFKGFWTYQFDPKATFKAPFFLNDNDKVDVDFMKIKKHFKYGRFDD
LDATALELPYKDSDITMLIILPNKRTGLAELESKLDTIDFNELTTKMYSEEVNVELPKFK
IEFDIELTEPLKKMGMEKMFSDAAQFDELLTSTEPLKVSQVVHKAFIEVNEEGAEAAAAT
AMIMMSRCAMISRSQQFIANRPFIFALKFVADALFVGRIENFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2453.t114 CDD cd19601 serpin42Da-like 39 398 4.66974E-154
8 g2453.t114 Gene3D G3DSA:3.30.497.10 Antithrombin 55 346 1.7E-120
7 g2453.t114 Gene3D G3DSA:2.30.39.10 - 196 397 1.7E-120
2 g2453.t114 PANTHER PTHR11461 SERINE PROTEASE INHIBITOR, SERPIN 36 399 7.2E-90
3 g2453.t114 PANTHER PTHR11461:SF180 LEUKOCYTE ELASTASE INHIBITOR 36 399 7.2E-90
1 g2453.t114 Pfam PF00079 Serpin (serine protease inhibitor) 39 401 4.9E-111
10 g2453.t114 Phobius SIGNAL_PEPTIDE Signal peptide region 1 27 -
11 g2453.t114 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 10 -
12 g2453.t114 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 11 22 -
13 g2453.t114 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 23 27 -
9 g2453.t114 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 28 403 -
16 g2453.t114 ProSitePatterns PS00284 Serpins signature. 377 387 -
17 g2453.t114 SMART SM00093 serpin2 45 402 2.7E-121
4 g2453.t114 SUPERFAMILY SSF56574 Serpins 26 401 3.53E-119
6 g2453.t114 SignalP_EUK SignalP-noTM SignalP-noTM 1 27 -
15 g2453.t114 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 26 -
5 g2453.t114 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 27 -

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