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.t5 isoform g9940.t5 6117230 6118709
chr_1 g9940 g9940.t5 exon g9940.t5.exon1 6117230 6117483
chr_1 g9940 g9940.t5 exon g9940.t5.exon2 6117608 6117665
chr_1 g9940 g9940.t5 exon g9940.t5.exon3 6117760 6118134
chr_1 g9940 g9940.t5 cds g9940.t5.CDS1 6117830 6118134
chr_1 g9940 g9940.t5 exon g9940.t5.exon4 6118209 6118401
chr_1 g9940 g9940.t5 cds g9940.t5.CDS2 6118209 6118401
chr_1 g9940 g9940.t5 exon g9940.t5.exon5 6118480 6118645
chr_1 g9940 g9940.t5 cds g9940.t5.CDS3 6118480 6118645
chr_1 g9940 g9940.t5 exon g9940.t5.exon6 6118705 6118709
chr_1 g9940 g9940.t5 cds g9940.t5.CDS4 6118705 6118709
chr_1 g9940 g9940.t5 TSS g9940.t5 NA NA
chr_1 g9940 g9940.t5 TTS g9940.t5 NA NA

Sequences

>g9940.t5 Gene=g9940 Length=1051
AATTTATCGGTTAAAAAAATTCAAAAATTCGCAGTCCCCTATTTTCGCATCTTCTATAAG
TTTTTTGTGCCGCTGCTTCATAAAGAAATTTACGATTCTACAATCGATAAAAATTTTTAA
ATAAAAAGTGCTTGAGTTGTTTGCTAATCATTAAAACAAGATAAATCTGTGAAGAAACAT
TGGTTTCATTGAGAAAAACTAAATTGAATCTTTTACTGATAGTGATAAAGGATAAAAATA
AAAGAAAAACATTGGTTTTTGAATACATATATTACTGATTGATTCAACTAACAATATGGC
TGATCCAAAACAGTCTTAATAAAACAGAGGAGATGATTTAGCTACAGCAATTTTAAAGCA
AAAGTCTAAACCTAATCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGT
TTGTCTATCGCAAGCAAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTT
AAAGGGGAAAAGAAGAAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAA
TGAGAAAATTCGTATGAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATAT
TGTCGCCATTCAATCATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAAT
TGATGACACTGTCGAAGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTT
CCTCGAAGCTTATCGTCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAG
AGCTGTTGAATTTAAAGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGA
TACTGTAATTCATTGTGAAGGAGATCCGATTAAACGTGAAGAAGAAGAAGAAGCGTTGAA
TGCTGTCGGTTATGATGATATTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAAT
GGTCGAGTTACCATTGCGTCATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACG
AGGTATTTTGTTGTATGGACCACCAGGTACT

>g9940.t5 Gene=g9940 Length=223
MVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGKRRKETVCIVLSDDTCPNEKIRMNR
VVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDTVEGLTGNIFDVYLKPYFLEAYRPI
HKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVIHCEGDPIKREEEEEALNAVGYDDI
GGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g9940.t5 Gene3D G3DSA:2.40.40.20 - 1 81 0
11 g9940.t5 Gene3D G3DSA:3.10.330.10 - 82 177 0
10 g9940.t5 Gene3D G3DSA:3.40.50.300 - 178 223 0
3 g9940.t5 PANTHER PTHR23077:SF63 ZGC:136908 1 223 0
4 g9940.t5 PANTHER PTHR23077 AAA-FAMILY ATPASE 1 223 0
2 g9940.t5 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 2 80 0
1 g9940.t5 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 100 164 0
8 g9940.t5 SMART SM01073 CDC48_N_2 2 82 0
9 g9940.t5 SMART SM01072 CDC48_2_2 99 165 0
5 g9940.t5 SUPERFAMILY SSF50692 ADC-like 1 79 0
7 g9940.t5 SUPERFAMILY SSF54585 Cdc48 domain 2-like 81 171 0
6 g9940.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 162 223 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.

Raw TPM values