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.t9 TTS g13753.t9 32244371 32244371
chr_1 g13753 g13753.t9 isoform g13753.t9 32244504 32245453
chr_1 g13753 g13753.t9 exon g13753.t9.exon1 32244504 32244912
chr_1 g13753 g13753.t9 cds g13753.t9.CDS1 32244813 32244912
chr_1 g13753 g13753.t9 exon g13753.t9.exon2 32244973 32245311
chr_1 g13753 g13753.t9 cds g13753.t9.CDS2 32244973 32245311
chr_1 g13753 g13753.t9 exon g13753.t9.exon3 32245380 32245453
chr_1 g13753 g13753.t9 cds g13753.t9.CDS3 32245380 32245453
chr_1 g13753 g13753.t9 TSS g13753.t9 32245673 32245673

Sequences

>g13753.t9 Gene=g13753 Length=822
ATGGCTAACGTTTTAATTGCTGGGTACAATGAAATACCGATTGTTACAAGAATATATACA
ACAGCTTGTGTTTGCACAACATTTGCCGTTCATTTGGATTTAGTATCACCTTTTCAGTTA
TATTTCAATCCAAATTTAATTATGCAAGGACAAATTTGGCGACTCGTCACCACTTTTCTG
TTTTTCGGCACAATAGGATTTTCTTTTCTCTTTAATATGATTTTCACATATCGGTATTGC
CGTATGTTAGAAGAAGGATCATTTAGAGGAAAAACAGCAGATTTTATTATGATGTTCTTT
TTTGGAGCAGTTTTCATGATATTTTTTGCCTTCTTTATTAACCTTTTGTTCTTAGGACAG
GCATTTACTATTATGCTAGTTTATATTTGGTCTCGACGAAATCCTTTTCTAAGAATGAAT
TTTTTCGGATTGTTAAATTTTCAAGCACCTTACCTTCCATGGGTGTTATTGGCCTTTTCT
GTGATTTTGGGTGATATAAGTAAAATTTCTTAGATTAAGTCTTAATATAAATTAACTTAA
ATAATTTATCTATTTTATAATATAGGCAACGCCATCTACATTGATCTTGTTGGAATCGGA
GCAGGTCATTTCTACTATTTTCTTGAAGATGTGTTCCCCAATCAACCAAACGGTCGAAAA
TTACTCAAAACGCCACAATTTCTCAAAAACATCTTTGATGAACCAGTCGATACTGATGAT
TATATTGTTCTACCAGAAAATGATAGACCTGGAGGTGCTGCGTTTGCATGGGGAAATAAC
AACAATAATAATCCCAATAATAATAATGAGCAACCAAATTAA

>g13753.t9 Gene=g13753 Length=170
MANVLIAGYNEIPIVTRIYTTACVCTTFAVHLDLVSPFQLYFNPNLIMQGQIWRLVTTFL
FFGTIGFSFLFNMIFTYRYCRMLEEGSFRGKTADFIMMFFFGAVFMIFFAFFINLLFLGQ
AFTIMLVYIWSRRNPFLRMNFFGLLNFQAPYLPWVLLAFSVILGDISKIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13753.t9 PANTHER PTHR11009:SF5 DERLIN-2 6 165 8.6E-75
3 g13753.t9 PANTHER PTHR11009 DER1-LIKE PROTEIN, DERLIN 6 165 8.6E-75
1 g13753.t9 Pfam PF04511 Der1-like family 12 165 1.6E-58
10 g13753.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g13753.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 32 -
12 g13753.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 33 51 -
16 g13753.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 75 -
11 g13753.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 95 -
14 g13753.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 129 -
13 g13753.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 130 148 -
17 g13753.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 149 166 -
9 g13753.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 167 170 -
8 g13753.t9 SUPERFAMILY SSF144091 Rhomboid-like 10 164 1.23E-14
6 g13753.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
5 g13753.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
7 g13753.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
4 g13753.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -

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