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_2 g5818 g5818.t2 isoform g5818.t2 12057847 12059854
chr_2 g5818 g5818.t2 TSS g5818.t2 12057847 12057847
chr_2 g5818 g5818.t2 exon g5818.t2.exon1 12057847 12057912
chr_2 g5818 g5818.t2 exon g5818.t2.exon2 12058230 12058529
chr_2 g5818 g5818.t2 cds g5818.t2.CDS1 12058367 12058529
chr_2 g5818 g5818.t2 TTS g5818.t2 12058394 12058394
chr_2 g5818 g5818.t2 exon g5818.t2.exon3 12058723 12059030
chr_2 g5818 g5818.t2 cds g5818.t2.CDS2 12058723 12059027
chr_2 g5818 g5818.t2 exon g5818.t2.exon4 12059424 12059854

Sequences

>g5818.t2 Gene=g5818 Length=1105
CAGTCTGCGGTTGGAGTTAAAGGCGCAAAGTCGAGAAAAGTAAGTAGTGAAAGTGAAGTG
AGAACGTTTTTTTGTGCCTTTGATATTGTGTATTAATAAGAAAATTAAAAATTTATTAAT
TATGAAAATTTAAAATTGAAGACCTAAAAGGATAAATCATGAAAATAATTAAAAAATCAA
TTGTGATAATATGCATCGTCCTGATGCTTTTAAGCATTAGCGATGCAGCTGAAAAAAAGA
AGAAAAAATCTAGAAAATCCAAAACTGTACAAACACCTGTCATAAGACCACAAAGACAAC
AACCAGATTATTCAGATATTGAAAATATTGACACAAATTTCGACTATGATCAAAATGGAA
ATGAAGGTTCTGATAGAGTATCATCACAGCCCAATGAAAATCAATGGCAAAATGCACCAT
ATACTTGTCAATACAATGGTCGATGGTACAGAGAACGTGAAGAATTTAAATCTGGTCCAA
ATGATTGTATGACTTGTGTTTGTATTGATACTGAAGTTGCTTGTGATGACAGAGAATGTC
AAATTTCAACAACTGAATATCCACAATTTACTGATTTTGCTCGTGGTCCACCAAGATTTC
CTCAATCTAGACAAGAACAATTTGGTTCAAGAGCACAATCACAACAAACTCAAGGAGGTA
AAAAAGTTTAAAAAGACAACAAAAGACAGTTTTTTAAACTTCATCAAGTGCGAGAGTGTA
AAACAAGTGAAAAATTGCACAATTTGCTGATATTACGCGCAACTAATCATTGGACAATTG
TTGAAATTAAACTGCACTAACACAATCAAACAAAAAACGAGTTATTCTGACACTTTTGAG
TGTTTTTTTAAAAAAATTGAAAAGGGTTGAAAACCACATAAACATCATGCAACAAACAGC
AGTCATGTTTTTAATCTGTGTGTGTGAAAGAGGTCAAAGGGATTTGTTTGTATCAGATGA
GTTCATAAATATGACAAAATGCAGCTGTAAAGCAGCACTTGAAAAAATTATTTTAAAGTT
AATTACAAACGACAAGTGTGAATCATGTTGTAGCAAGAATTCAGAATTCTTATCAAATTT
TCTAAAAATAAAATTGTAAAATTTA

>g5818.t2 Gene=g5818 Length=155
MLLSISDAAEKKKKKSRKSKTVQTPVIRPQRQQPDYSDIENIDTNFDYDQNGNEGSDRVS
SQPNENQWQNAPYTCQYNGRWYREREEFKSGPNDCMTCVCIDTEVACDDRECQISTTEYP
QFTDFARGPPRFPQSRQEQFGSRAQSQQTQGGKKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5818.t2 Gene3D G3DSA:2.10.70.10 Complement Module 74 109 3.9E-5
3 g5818.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 71 -
6 g5818.t2 MobiDBLite mobidb-lite consensus disorder prediction 22 71 -
5 g5818.t2 MobiDBLite mobidb-lite consensus disorder prediction 125 155 -
4 g5818.t2 MobiDBLite mobidb-lite consensus disorder prediction 135 155 -
1 g5818.t2 Pfam PF00093 von Willebrand factor type C domain 75 117 4.8E-7
2 g5818.t2 SUPERFAMILY SSF57603 FnI-like domain 73 120 7.74E-9

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5818/g5818.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5818.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

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