Gene loci information

Transcript annotation

  • This transcript has been annotated as Transitional endoplasmic reticulum ATPase.

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 g9940 g9940.t13 TSS g9940.t13 6117534 6117534
chr_1 g9940 g9940.t13 isoform g9940.t13 6117649 6118893
chr_1 g9940 g9940.t13 exon g9940.t13.exon1 6117649 6117665
chr_1 g9940 g9940.t13 cds g9940.t13.CDS1 6117649 6117665
chr_1 g9940 g9940.t13 exon g9940.t13.exon2 6117775 6118134
chr_1 g9940 g9940.t13 cds g9940.t13.CDS2 6117775 6118134
chr_1 g9940 g9940.t13 exon g9940.t13.exon3 6118209 6118401
chr_1 g9940 g9940.t13 cds g9940.t13.CDS3 6118209 6118401
chr_1 g9940 g9940.t13 exon g9940.t13.exon4 6118490 6118645
chr_1 g9940 g9940.t13 cds g9940.t13.CDS4 6118490 6118498
chr_1 g9940 g9940.t13 exon g9940.t13.exon5 6118705 6118893
chr_1 g9940 g9940.t13 TTS g9940.t13 NA NA

Sequences

>g9940.t13 Gene=g9940 Length=915
ATGGCTGATCCAAAACAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAA
CCTAATCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCG
CAAGCAAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAA
AGAAGAAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATT
CGTATGAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATT
CAATCATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACT
GTCGAAGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCT
TATCGTCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAA
TTTAAAGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATT
CATTGTGAAGGAGATCCGATTAAACGTGAAAAGCGTTGAATGCTGTCGGTTATGATGATA
TTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATTGCGTC
ATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTATGGAC
CACCAGGTACTGGAAAAACTTTAATTGCAAGAGCTGTAGCAAATGAGACTGGCGCTTTCT
TCTTCTTAATTAATGGTCCTGAGATTATGTCTAAATTAGCTGGTGAATCAGAATCAAATT
TGCGTAAAGCATTCGAAGAAGCAGATAAGAATTCACCTGCAATTATATTTATTGATGAAT
TGGATGCAATTGCTC

>g9940.t13 Gene=g9940 Length=192
MADPKQGDDLATAILKQKSKPNRLMVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGK
RRKETVCIVLSDDTCPNEKIRMNRVVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDT
VEGLTGNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVI
HCEGDPIKREKR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g9940.t13 Gene3D G3DSA:2.40.40.20 - 1 105 0
9 g9940.t13 Gene3D G3DSA:3.10.330.10 - 106 190 0
3 g9940.t13 PANTHER PTHR23077:SF69 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE 5 191 0
4 g9940.t13 PANTHER PTHR23077 AAA-FAMILY ATPASE 5 191 0
2 g9940.t13 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 23 104 0
1 g9940.t13 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 124 188 0
7 g9940.t13 SMART SM01073 CDC48_N_2 23 106 0
8 g9940.t13 SMART SM01072 CDC48_2_2 123 189 0
5 g9940.t13 SUPERFAMILY SSF50692 ADC-like 20 103 0
6 g9940.t13 SUPERFAMILY SSF54585 Cdc48 domain 2-like 105 191 0

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