Gene loci information

Transcript annotation

  • This transcript has been annotated as Derlin-2.

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 g13753 g13753.t11 TTS g13753.t11 32244371 32244371
chr_1 g13753 g13753.t11 isoform g13753.t11 32244504 32245980
chr_1 g13753 g13753.t11 exon g13753.t11.exon1 32244504 32244760
chr_1 g13753 g13753.t11 cds g13753.t11.CDS1 32244504 32244760
chr_1 g13753 g13753.t11 exon g13753.t11.exon2 32244836 32244912
chr_1 g13753 g13753.t11 cds g13753.t11.CDS2 32244836 32244912
chr_1 g13753 g13753.t11 exon g13753.t11.exon3 32244973 32245311
chr_1 g13753 g13753.t11 cds g13753.t11.CDS3 32244973 32245311
chr_1 g13753 g13753.t11 exon g13753.t11.exon4 32245380 32245481
chr_1 g13753 g13753.t11 cds g13753.t11.CDS4 32245380 32245453
chr_1 g13753 g13753.t11 exon g13753.t11.exon5 32245845 32245980
chr_1 g13753 g13753.t11 TSS g13753.t11 NA NA

Sequences

>g13753.t11 Gene=g13753 Length=911
TCTATAGTTTAAGAAAAATATTGTTTTGATTATTATTTTTGCAAAAACAAATGTTTATTT
TATATTATCAATAGATTGAATTGATGCAAACAAGTTACAATACACTTACTGTATTACACT
GCATTTAATAAACTTGAACCTTGTGAAATTAAAGGTGAAAACAAATGGCTAACGTTTTAA
TTGCTGGGTACAATGAAATACCGATTGTTACAAGAATATATACAACAGCTTGTGTTTGCA
CAACATTTGCCGTTCATTTGGATTTAGTATCACCTTTTCAGTTATATTTCAATCCAAATT
TAATTATGCAAGGACAAATTTGGCGACTCGTCACCACTTTTCTGTTTTTCGGCACAATAG
GATTTTCTTTTCTCTTTAATATGATTTTCACATATCGGTATTGCCGTATGTTAGAAGAAG
GATCATTTAGAGGAAAAACAGCAGATTTTATTATGATGTTCTTTTTTGGAGCAGTTTTCA
TGATATTTTTTGCCTTCTTTATTAACCTTTTGTTCTTAGGACAGGCATTTACTATTATGC
TAGTTTATATTTGGTCTCGACGAAATCCTTTTCTAAGAATGAATTTTTTCGGATTGTTAA
ATTTTCAAGCACCTTACCTTCCATGGGTGTTATTGGCCTTTTCTGTGATTTTGGGCAACG
CCATCTACATTGATCTTGTTGGAATCGGAGCAGGTCATTTCTACTATTTTCTTGAAGATG
TGTTCCCCAATCAACCAAACGGTCGAAAATTACTCAAAACGCCACAATTTCTCAAAAACA
TCTTTGATGAACCAGTCGATACTGATGATTATATTGTTCTACCAGAAAATGATAGACCTG
GAGGTGCTGCGTTTGCATGGGGAAATAACAACAATAATAATCCCAATAATAATAATGAGC
AACCAAATTAA

>g13753.t11 Gene=g13753 Length=248
MANVLIAGYNEIPIVTRIYTTACVCTTFAVHLDLVSPFQLYFNPNLIMQGQIWRLVTTFL
FFGTIGFSFLFNMIFTYRYCRMLEEGSFRGKTADFIMMFFFGAVFMIFFAFFINLLFLGQ
AFTIMLVYIWSRRNPFLRMNFFGLLNFQAPYLPWVLLAFSVILGNAIYIDLVGIGAGHFY
YFLEDVFPNQPNGRKLLKTPQFLKNIFDEPVDTDDYIVLPENDRPGGAAFAWGNNNNNNP
NNNNEQPN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13753.t11 PANTHER PTHR11009:SF5 DERLIN-2 7 235 2.4E-102
3 g13753.t11 PANTHER PTHR11009 DER1-LIKE PROTEIN, DERLIN 7 235 2.4E-102
1 g13753.t11 Pfam PF04511 Der1-like family 12 201 3.2E-73
9 g13753.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g13753.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 32 -
12 g13753.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 33 51 -
16 g13753.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 77 -
10 g13753.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 97 -
15 g13753.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 98 131 -
13 g13753.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 132 150 -
14 g13753.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 171 -
11 g13753.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 172 248 -
8 g13753.t11 SUPERFAMILY SSF144091 Rhomboid-like 10 189 1.31E-16
7 g13753.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
6 g13753.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
5 g13753.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 130 -
4 g13753.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 172 -

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

Pathway

  • This transcript belongs to the following pathways

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