Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Integrin beta-PS.

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_1 g13034 g13034.t4 isoform g13034.t4 27634379 27636423
chr_1 g13034 g13034.t4 exon g13034.t4.exon1 27634379 27634609
chr_1 g13034 g13034.t4 cds g13034.t4.CDS1 27634522 27634609
chr_1 g13034 g13034.t4 exon g13034.t4.exon2 27634673 27634782
chr_1 g13034 g13034.t4 cds g13034.t4.CDS2 27634673 27634782
chr_1 g13034 g13034.t4 exon g13034.t4.exon3 27634842 27635030
chr_1 g13034 g13034.t4 cds g13034.t4.CDS3 27634842 27635030
chr_1 g13034 g13034.t4 exon g13034.t4.exon4 27635091 27636423
chr_1 g13034 g13034.t4 cds g13034.t4.CDS4 27635091 27635156
chr_1 g13034 g13034.t4 TSS g13034.t4 NA NA
chr_1 g13034 g13034.t4 TTS g13034.t4 NA NA

Sequences

>g13034.t4 Gene=g13034 Length=1863
TTTGTTCTGGTCATGGAAGTTGCGTTTGTGGTCGATGCGAGTGTGAAATTAAAGAAGATG
TGAGATACTCAGGAAAATATTGTGAAAAATGCCCAACATGTCCAGGACGTTGCGATGAAT
TGAGAGCTTGTGTTGAATGTCAAATGTACAAGAAAGGACCATTGAAAGATGAAAAAGATT
GTGCCAGCAATTGCACTTTGTTTGTGCCAATTTCAGTTGAACATGTTGAATATAATGAAG
ACGAAGATGAACATCTTTGTACATTCTACGATGAAGATGAATGTCGCTATCGTTTTGTTT
ATAATGAAACTGTTGAAAAGAATGGAACTGTTACATTACATGTTCGTGCACAAGAAAATC
CAGAATGTCCACCAAAAGTCTTTTTACTTGGAATTGTTCTTGGTGTTATTGCTGCTATTG
TATTGATTGGTATGGCAATGTTGCTACTTTGGAAACTTCTTACAACTATTCATGATAGAC
GAGAATTTGCTAGATTCGAGAAAGAACGAATGATGGCCAAATGGGATACTGGTGAAAATC
CAATTTATAAACAAGCAACATCAACTTTCAAAAATCCAACATATGCTGGAAAATAAATGA
GCAATTTTTGACCTCGGTCTGGTATCGAAAAGTCACAACTGCCATAAAAAAATTCATCCT
AAAAACCTCTTTTGTCGTAAAATCACATGAAATTCAACAAAATTGTGATTGAACATCTTT
TCAAATGATCGAATATTTTTATAATTTGATCGTAAAAAACAACAACTTTGGACTTAGCGG
AAATATCGCTAATTTGTGAATAATTTTGAATATAAAAGTCATTAACAGAGACCATACAAA
TAATTGTGTCTCAACAGGAAATATTAAAAATGAAACTTTTAAGGCCTTAGCGATAAAAGT
GTCTTTTGCAATTGATAAAAAATCTTTAGTCATTTTACATGAAATTTACAAATTTTAACG
AGAAAAAAATTTGCGCACATTTTTACCAATTTCATAAAAATCATTAATATAAAGTGAAAG
AAAAACTTAACATAGATACAACTATATAAATTAAAAAAGAAGTTTTTTAAATTGGAAATA
ACAAAATTGACAAACATTAAAATTTTTGAATTTAGGGTTCATGTTTGTGATGATAAACAT
GAAAACTTAACAAAATATCACCAAAAAATAAGAATTTTGATGAAAAAAAAAGAAACTCGA
GTGTTATAAAATAAAAATTATTAGTATTTTGCTGTACTTAGACGAGACATGATCAAATTG
ATTAATATATAACAAAAAATTCAATCTTATTAATTTTAAAAGCAATATTTTTTGCTAACT
CTAATCGTCAATCGATGTCGAACCGTTAAAAGTAATAATAATTAATAAATTAATTTTATC
TAGATGCCAAATTTATGAATGAACGTATGAATGTATTTTAACTTTATTTTTTTTTTACAA
AACTAATCAACTCTCTTGACTAATAATTTTTCTTAAGCATAAGAAACTTTTCATACTTTT
TTTATTTTTATAAATTTTTTTGTGTTTCTTTCTTTAGTTTTCTAATTATCTTTAATAATT
TTTAGTTAAGCTGTTTAAACTAAATAAATGAATTATTATGAAAATTAAATGCTTGTAACT
TTTTTCTGTGCCTTTACTTATCTAATTATGAAACGAAATTATAATAAAGAGAAGACAAAA
TTAAAATGAAAAATTTACTTTTTTATTTTCTTTAAACTTACAGCATTTCATCTTAAAGAC
AAGGTTTTAAAGAAAATGATTTTTTTCTGAAATTTCAATATGAAGTTTAAAGTCTTAAAA
TTTTTTTGAAAAAAACAATTTATTTAAATTTGTATATAAATAAAATAAATTTTATTAGCC
ATT

>g13034.t4 Gene=g13034 Length=150
MYKKGPLKDEKDCASNCTLFVPISVEHVEYNEDEDEHLCTFYDEDECRYRFVYNETVEKN
GTVTLHVRAQENPECPPKVFLLGIVLGVIAAIVLIGMAMLLLWKLLTTIHDRREFARFEK
ERMMAKWDTGENPIYKQATSTFKNPTYAGK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13034.t4 Coils Coil Coil 149 150 -
10 g13034.t4 Gene3D G3DSA:3.10.450.180 - 1 76 1.4E-12
9 g13034.t4 Gene3D G3DSA:1.20.5.100 - 77 150 5.4E-36
3 g13034.t4 PANTHER PTHR10082 INTEGRIN BETA SUBUNIT 2 149 3.4E-37
4 g13034.t4 PANTHER PTHR10082:SF25 INTEGRIN BETA-3 2 149 3.4E-37
5 g13034.t4 PRINTS PR01186 Integrin beta subunit signature 79 96 6.0E-18
6 g13034.t4 PRINTS PR01186 Integrin beta subunit signature 96 114 6.0E-18
7 g13034.t4 PRINTS PR01186 Integrin beta subunit signature 131 141 6.0E-18
2 g13034.t4 Pfam PF07965 Integrin beta tail domain 2 77 1.5E-12
1 g13034.t4 Pfam PF08725 Integrin beta cytoplasmic domain 104 147 8.2E-26
13 g13034.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 78 -
14 g13034.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 79 103 -
12 g13034.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 104 150 -
16 g13034.t4 SMART SM01242 Integrin_B_tail_2 1 80 1.4E-11
17 g13034.t4 SMART SM01241 Integrin_b_cyt_2 104 150 2.8E-31
8 g13034.t4 SUPERFAMILY SSF69687 Integrin beta tail domain 2 77 8.24E-11
15 g13034.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -

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:0008305 integrin complex CC
GO:0007155 cell adhesion BP
GO:0005178 integrin binding MF
GO:0007229 integrin-mediated signaling pathway BP
GO:0070527 platelet aggregation 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.

Raw TPM values