Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g12784 g12784.t2 TTS g12784.t2 26126502 26126502
chr_1 g12784 g12784.t2 isoform g12784.t2 26126804 26129120
chr_1 g12784 g12784.t2 exon g12784.t2.exon1 26126804 26127174
chr_1 g12784 g12784.t2 cds g12784.t2.CDS1 26126804 26127174
chr_1 g12784 g12784.t2 exon g12784.t2.exon2 26128720 26129120
chr_1 g12784 g12784.t2 cds g12784.t2.CDS2 26128720 26128981
chr_1 g12784 g12784.t2 TSS g12784.t2 NA NA

Sequences

>g12784.t2 Gene=g12784 Length=772
GTCAGATGACAATGGTGAGGAATGTAATGGTCATGCATTATTTTGTGATTGCGGTGTTTG
TCAGTGTCAACCAGAATTTACTGGACCAACATGTGAATGTTCAACATTGCAGACCAATTG
CATTAGTCCAGATAGCAAAATGTCAAATGATGGTGGAAAAATCTGTTCAGGGCATGGAAC
GTGCAAATGCAATCAATGCGAGTGTGAAGATTCGCGTACTGGAAAATTCTGTGAAAGCAC
ACCCGGGAATGAGACATTTAATTCATTGTGTATATTCTATGAAACGTGCGTACAATGTGT
CATAAACCGTAAACTGCAACACGAGTGCTCGGATTATGAGCAAAAATGTTCCTCGCAGAA
TGGTTTGCTGTATAAATCAGAATTTTATGACAAAATCTCAGATGCAGATATTTTATGTAT
AGCGCGTGTGAGATATGATGATGACACAGTTTGCGAATATAAATTTACGTATGAATTGGA
TGAAAAATCAGAGACAAATCTTCGTATTGAGAACACAGATTGTCCGCCAGTGAATGTTGC
TGCATATTCAATTATTGGCATAATCGTTGCGACATTTCTCATTGGATTTCTCATTTTGAT
GGTAATCAAGTGCAACATGTATATCGCGGAAAAGCGAGAATTTGCTGCATTTGAAAAAGA
ACGAGATCAACAAACCGAATATAAGTATGAAAGTCCACTATATAAATCACCAGTGACAAC
ATTCCGTAATCCACAATCTACATCACAATCGAATGCTTTCGAAATGAAATAA

>g12784.t2 Gene=g12784 Length=210
MSNDGGKICSGHGTCKCNQCECEDSRTGKFCESTPGNETFNSLCIFYETCVQCVINRKLQ
HECSDYEQKCSSQNGLLYKSEFYDKISDADILCIARVRYDDDTVCEYKFTYELDEKSETN
LRIENTDCPPVNVAAYSIIGIIVATFLIGFLILMVIKCNMYIAEKREFAAFEKERDQQTE
YKYESPLYKSPVTTFRNPQSTSQSNAFEMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12784.t2 Gene3D G3DSA:2.10.25.10 Laminin 1 58 4.5E-9
11 g12784.t2 Gene3D G3DSA:1.20.5.100 - 126 201 8.3E-17
3 g12784.t2 PANTHER PTHR10082:SF59 INTEGRIN BETA-NU 6 202 2.9E-47
4 g12784.t2 PANTHER PTHR10082 INTEGRIN BETA SUBUNIT 6 202 2.9E-47
6 g12784.t2 PRINTS PR01186 Integrin beta subunit signature 9 22 4.7E-11
5 g12784.t2 PRINTS PR01186 Integrin beta subunit signature 132 149 4.7E-11
8 g12784.t2 PRINTS PR01186 Integrin beta subunit signature 149 167 4.7E-11
7 g12784.t2 PRINTS PR01186 Integrin beta subunit signature 184 194 4.7E-11
1 g12784.t2 Pfam PF07974 EGF-like domain 4 31 3.6E-6
2 g12784.t2 Pfam PF08725 Integrin beta cytoplasmic domain 157 198 1.4E-9
13 g12784.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 132 -
14 g12784.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 133 156 -
12 g12784.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 157 210 -
16 g12784.t2 ProSitePatterns PS00243 Integrins beta chain cysteine-rich domain signature. 9 22 -
17 g12784.t2 SMART SM01241 Integrin_b_cyt_2 157 203 6.5E-8
9 g12784.t2 SUPERFAMILY SSF57196 EGF/Laminin 4 35 5.58E-6
15 g12784.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 156 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed