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.t128 TTS g2453.t128 18037381 18037381
chr_3 g2453 g2453.t128 isoform g2453.t128 18037487 18042146
chr_3 g2453 g2453.t128 exon g2453.t128.exon1 18037487 18037677
chr_3 g2453 g2453.t128 cds g2453.t128.CDS1 18037556 18037677
chr_3 g2453 g2453.t128 exon g2453.t128.exon2 18038878 18039019
chr_3 g2453 g2453.t128 cds g2453.t128.CDS2 18038878 18039019
chr_3 g2453 g2453.t128 exon g2453.t128.exon3 18039101 18039684
chr_3 g2453 g2453.t128 cds g2453.t128.CDS3 18039101 18039684
chr_3 g2453 g2453.t128 exon g2453.t128.exon4 18039768 18039975
chr_3 g2453 g2453.t128 cds g2453.t128.CDS4 18039768 18039975
chr_3 g2453 g2453.t128 exon g2453.t128.exon5 18040042 18040157
chr_3 g2453 g2453.t128 cds g2453.t128.CDS5 18040042 18040157
chr_3 g2453 g2453.t128 exon g2453.t128.exon6 18041800 18042146
chr_3 g2453 g2453.t128 cds g2453.t128.CDS6 18041800 18041830
chr_3 g2453 g2453.t128 TSS g2453.t128 18042146 18042146

Sequences

>g2453.t128 Gene=g2453 Length=1588
GTTTGAAATCGTTCATTGAGAAAAGAACACGTGAAAAAAAAATAATTTAGTCACAAATCA
GTAAAATTGTTGTGATAAATTTTCCATTAATTTCCTAGTTTTTTTAAGTTAATATTTACA
AAGGCCATTATGTCAAATAAAAAATTTAATGTCACAAACTAATTGAATTTTAGCTACTGA
TGGTTTTTATGATTATTAGTGTGAAAAATACCAAATACGAGCCAAATAATATTATTGAAC
TTGAGTGAGCTTATATAAACATATATTGTCGTCATTAACATTTACTGTTTAGAAAAAAAT
TACTGAAATCAGAAATATGATTTTATCAAAACTTGTTAATAAAACATTAATTCTCTCAGT
TTGTGCTCTGACTATCGTGCTAAACGCATCAATGGCGTCACCCTCTGAAATCGAACAAAA
GTTTTCAAAATCAGCCAGCAACTTTGCTGCTAAATTGTACCAAAACTCAATTCAAGGAAA
AACTGGCAATGTAATTATTTCACCTGTCTCAGTTCAAACAGCCGTCACTTTGGCTATGTT
TGGTGCTGCTGGTGAGACCAAGCAAGAAATGTTAAAAGGTCTCGAATATCAGGGTTTCAC
TGATCAAATAATTGCTGATAACTATCAACGATTTGGCGAGAGCGTCGCAAAGACTAATGG
ATTGAAAATCGCTAATAAGATTTATGTGATGAAAGGCTATTCAGTCAAGCCAACATTCCA
GCAAGTCGCAACAAAGAGTTTCAATTCAGAAGCTGAAGATGTAAATTTCGCACAAAGTAA
AGACTCAGCTGGCAAAATCAATACATGGGTTGAAAATCAAACAAATAATAAAATTAAAAA
TCTTATCTCACCTGATTCATTGGATGCTGACACACGTATGGTTCTTGTAAATGCCATTTA
CTTCAAAGGATTCTGGACCTATCAATTTGATCCAAAAGCAACATTCAAAGCACCATTCTT
TCTCAATGATAATGATAAAGTTGATGTTGATTTCATGAAAATTAAGAAACATTTCAAATA
TGGACGATTTGATGATCTTGATGCAACTGCATTGGAATTGCCTTACAAAGATTCTGATAT
TACAATGTTGATAATTTTACCAAATAAACGCACTGGATTGGCTGAATTGGAGAGCAAATT
GGACACAATTGACTTCAATGAGCTCACAACAAAGATGTATTCGGAAGAAGTTAATGTTGA
ATTGCCAAAGTTTAAAATTGAATTTGACATTGAATTGACCGAGCCATTAAAGAAGATGGG
AATGGAGAAAATGTTCTCAGATGCTGCTCAATTTGATGAATTGCTTACATCGACTGAACC
TCTCAAGGTTTCACAAGTTGTTCATAAAGCCTTCATTGAAGTCAATGAAGAAGGTGCTGA
AGCAGCTGCTGCTACAGGCATGATTTTTATGCAATGCAGCCTTAGGGAAAATCCATCTTT
TAAAGTTAATCATCCGTTTTTATTTGTTCTAAAAACACCTTTGGGTTCTTACTTCATTGG
ACGATTGCAAAACTTTTAAAAATTCAACAAATACAATTTATTATTAATTAAATTTGTTCA
TAATAAAAAAATGACGTTTTCAAGTAGG

>g2453.t128 Gene=g2453 Length=400
MILSKLVNKTLILSVCALTIVLNASMASPSEIEQKFSKSASNFAAKLYQNSIQGKTGNVI
ISPVSVQTAVTLAMFGAAGETKQEMLKGLEYQGFTDQIIADNYQRFGESVAKTNGLKIAN
KIYVMKGYSVKPTFQQVATKSFNSEAEDVNFAQSKDSAGKINTWVENQTNNKIKNLISPD
SLDADTRMVLVNAIYFKGFWTYQFDPKATFKAPFFLNDNDKVDVDFMKIKKHFKYGRFDD
LDATALELPYKDSDITMLIILPNKRTGLAELESKLDTIDFNELTTKMYSEEVNVELPKFK
IEFDIELTEPLKKMGMEKMFSDAAQFDELLTSTEPLKVSQVVHKAFIEVNEEGAEAAAAT
GMIFMQCSLRENPSFKVNHPFLFVLKTPLGSYFIGRLQNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2453.t128 CDD cd19601 serpin42Da-like 39 396 3.81383E-156
8 g2453.t128 Gene3D G3DSA:3.30.497.10 Antithrombin 55 346 1.9E-121
7 g2453.t128 Gene3D G3DSA:2.30.39.10 - 196 389 1.9E-121
2 g2453.t128 PANTHER PTHR11461 SERINE PROTEASE INHIBITOR, SERPIN 36 397 2.3E-91
3 g2453.t128 PANTHER PTHR11461:SF180 LEUKOCYTE ELASTASE INHIBITOR 36 397 2.3E-91
1 g2453.t128 Pfam PF00079 Serpin (serine protease inhibitor) 39 388 9.6E-112
10 g2453.t128 Phobius SIGNAL_PEPTIDE Signal peptide region 1 27 -
11 g2453.t128 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 10 -
12 g2453.t128 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 11 22 -
13 g2453.t128 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 23 27 -
9 g2453.t128 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 28 400 -
16 g2453.t128 ProSitePatterns PS00284 Serpins signature. 375 385 -
17 g2453.t128 SMART SM00093 serpin2 45 395 1.8E-120
4 g2453.t128 SUPERFAMILY SSF56574 Serpins 26 397 1.2E-118
6 g2453.t128 SignalP_EUK SignalP-noTM SignalP-noTM 1 27 -
15 g2453.t128 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 26 -
5 g2453.t128 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