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_3 g3960 g3960.t2 TSS g3960.t2 29279442 29279442
chr_3 g3960 g3960.t2 isoform g3960.t2 29279504 29280886
chr_3 g3960 g3960.t2 exon g3960.t2.exon1 29279504 29279630
chr_3 g3960 g3960.t2 cds g3960.t2.CDS1 29279504 29279630
chr_3 g3960 g3960.t2 exon g3960.t2.exon2 29279693 29280886
chr_3 g3960 g3960.t2 cds g3960.t2.CDS2 29279693 29280885
chr_3 g3960 g3960.t2 TTS g3960.t2 NA NA

Sequences

>g3960.t2 Gene=g3960 Length=1321
ATGTCTAAAATCGATGAAGAAGAAATTGTGAAAGCACTTAGTTTAGAGGAAGCAGCTCTT
AATGAGTTTAAAAGACGGAAAAATTCGTGTCCAGCTCCACAGAGTCACTCGAAAATTGCT
TTAAATGACAATAAACCAAATAATTCACTCTATTCATCATCTTCATCATCAAATATTTCA
AGACCAATTGATGAGTTAGATTTAATTTCATTCACTAGTGATATTCAAGAAAGTGCTCAT
AATGCAAGAAAAAAAACTGATGACGATCATTTTAATAAGCTTAAAGAGTCAATATTAAAG
TTAAACGATAATCGTAATCAGCTGCAAAAGCAACTAGTTCCATATAACAATCCTAATCAT
ATATATAGTGGAACAAATAATGTTAATCAGTTTTACAGTCAACAAATGTATTTCAATTCA
TCGCCTTATTCGCAAATTCCGAGAATCGGATTTGAAAACTTTATGCCTTATGGATTTCAT
TCACCGCAGCAGCAGCACCAGCTACAACAACAACAAACTTATGCATTTTCTCCACAACAA
TCTCAAATATGGAATCGCCCTTCAATTCAAGCAGCTTCTAATTCTTCTTCATCTTCTACT
AACACAATTTATTCGCCTCTATCTACATCTTCACAAAGTTTAGTAAGAAGCCAAACGAGA
TTATCAGAAACAAATTTGGCCATAAGAAAACCCGAGTCTGTTAAATCGTCACAGCAAAGC
AGCAATAATAATTCATCATTATCAACAATAAAAGATTTGATAAATTTAGATGATGCTGAT
GATTTAAATTTCATCGCAAATATTTTACAAGCTTTTGATCCGCTAATTGCCAAAAATGAA
GAAGCAAGTAATTCTTATTATTCGGATCAAGATCCTTTTGACTATATATATAGCGGTGGA
ACACAATACTCAGATCCACTCTATGAAGCAGTCATTCGAAGTGATCGTTCAGTCATTTCA
CCAAAAAATCATTCAGATCAAGATATATGTCAATATTACATAGCAGCATCTTCATCACCT
TCAACTTTACATAGGAAAATTGAAGAAACAAGTAATGAACAAGAACCACCACCATTACCA
CCTCGAAATTCATCGAGAACAGTTCAAGAAGAGACGTCGACTAGTCAACAAATTTATAAC
AATCAATACTCGAAAAAATTGTATGAAAACATTGTAGAATGTAGAAAATTTGATAAAGAT
TCTTTGGCATTCTACACAATGGTAAAAGAATTGCGATCGAAGTATCTTTATAATGATTAT
ACTTCAAACATAGGTCATATTGTTGCAGCTAAACTTGATAGCAAATATCTCAATGTATCA
A

>g3960.t2 Gene=g3960 Length=440
MSKIDEEEIVKALSLEEAALNEFKRRKNSCPAPQSHSKIALNDNKPNNSLYSSSSSSNIS
RPIDELDLISFTSDIQESAHNARKKTDDDHFNKLKESILKLNDNRNQLQKQLVPYNNPNH
IYSGTNNVNQFYSQQMYFNSSPYSQIPRIGFENFMPYGFHSPQQQHQLQQQQTYAFSPQQ
SQIWNRPSIQAASNSSSSSTNTIYSPLSTSSQSLVRSQTRLSETNLAIRKPESVKSSQQS
SNNNSSLSTIKDLINLDDADDLNFIANILQAFDPLIAKNEEASNSYYSDQDPFDYIYSGG
TQYSDPLYEAVIRSDRSVISPKNHSDQDICQYYIAASSSPSTLHRKIEETSNEQEPPPLP
PRNSSRTVQEETSTSQQIYNNQYSKKLYENIVECRKFDKDSLAFYTMVKELRSKYLYNDY
TSNIGHIVAAKLDSKYLNVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g3960.t2 Coils Coil Coil 91 111 -
1 g3960.t2 MobiDBLite mobidb-lite consensus disorder prediction 26 56 -
4 g3960.t2 MobiDBLite mobidb-lite consensus disorder prediction 28 56 -
3 g3960.t2 MobiDBLite mobidb-lite consensus disorder prediction 225 245 -
2 g3960.t2 MobiDBLite mobidb-lite consensus disorder prediction 343 376 -

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