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 g9948 g9948.t9 isoform g9948.t9 6138816 6140365
chr_1 g9948 g9948.t9 exon g9948.t9.exon1 6138816 6139041
chr_1 g9948 g9948.t9 cds g9948.t9.CDS1 6138822 6139041
chr_1 g9948 g9948.t9 exon g9948.t9.exon2 6139590 6140365
chr_1 g9948 g9948.t9 cds g9948.t9.CDS2 6139590 6139675
chr_1 g9948 g9948.t9 TSS g9948.t9 NA NA
chr_1 g9948 g9948.t9 TTS g9948.t9 NA NA

Sequences

>g9948.t9 Gene=g9948 Length=1002
AAAAAAATGTTTCCGCTTAATTTAGGAATTCTTATCGGAGGAATTCTAACGACAGGTGCA
ATGGGTGATCGTCTACAAGTGCCTAATGTGATTCTTCAGGGTTTCGCTACCGGAACTCTA
TTATATGTGATTTTCTTTGAAGTTCTCTCCAAAGATCGTTCGGGAATGCTTCCTTATTTG
AGTGTATTTGCCGGATTTGTCATTATGACTGGCCTACAATATATCGCTGGTGTAACTGAA
AATCAAGGATTGACGGTTTTAATCCCAGACGATGTATTAACAACACTTGATCAAAATCAT
GCACATGGGTAATTTTTTTATAAATCGAAAAATAGACATTGAGATAAACAGTAACGTGCA
CGATATCATAAAGGATCTTCAATTATCTGCACGTTTCACCACTTAACAACAAAGTTTATC
ATTTTGTCGATTTTCTCCTATAGGAGATAATTACGTGTTCCCCTCATGCTGATATCAAAC
CTTTAAGTGAAGTTTAAAATGAAAGTGCCAATTTCAACATTTAAGTACGTTATTATTATA
GAAACTCCTTTTTTCTTCCTTCAATTAAGTGATAAGATTTAAAGTCATTGTAAAAAGAAA
AGCACATGTTATTTTATCATCATCAAAATTTTTGTACATTAATCAGGGACTTGAGTTAAA
ATAACTTTATAAAGTAGATGAGAACTTATAAAATCCACTAGGCGAAAAACATGAATGAAT
CATATTTATTTGTGTATTTTGAAATATATGATGGTTGTGATCGCTATTATGAATGTGTGT
AGTTCATAAACATTTTCAATATTTCCTTATAGATTAAGTAGAGTGTACATAAATAGTAAA
ATATTTTAGTAAATGTAAATTTTTTAGCTAATAAATCAAGACTTTATTATTTAAAAACTT
GAATTTATCATAAAAAATTTTTTTAAATTCTTTCACCTCGGTTTATAGATAACTTTTTAT
TACAGCTCTAATTGAGTACCATATCATTCAGTTTATGATAAT

>g9948.t9 Gene=g9948 Length=101
MFPLNLGILIGGILTTGAMGDRLQVPNVILQGFATGTLLYVIFFEVLSKDRSGMLPYLSV
FAGFVIMTGLQYIAGVTENQGLTVLIPDDVLTTLDQNHAHG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9948.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
8 g9948.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
9 g9948.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
12 g9948.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
5 g9948.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 29 -
10 g9948.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 47 -
4 g9948.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 53 -
11 g9948.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 74 -
6 g9948.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 75 101 -
3 g9948.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 19 -
2 g9948.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 48 -
1 g9948.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -

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.

Raw TPM values