Gene loci information

Transcript annotation

  • This transcript has been annotated as Hydroxysteroid dehydrogenase-like protein 1.

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_2 g4622 g4622.t2 TTS g4622.t2 3658632 3658632
chr_2 g4622 g4622.t2 isoform g4622.t2 3658693 3660327
chr_2 g4622 g4622.t2 exon g4622.t2.exon1 3658693 3658797
chr_2 g4622 g4622.t2 cds g4622.t2.CDS1 3658693 3658797
chr_2 g4622 g4622.t2 exon g4622.t2.exon2 3658855 3659057
chr_2 g4622 g4622.t2 cds g4622.t2.CDS2 3658855 3659057
chr_2 g4622 g4622.t2 exon g4622.t2.exon3 3659118 3659474
chr_2 g4622 g4622.t2 cds g4622.t2.CDS3 3659118 3659474
chr_2 g4622 g4622.t2 exon g4622.t2.exon4 3659585 3659707
chr_2 g4622 g4622.t2 cds g4622.t2.CDS4 3659585 3659707
chr_2 g4622 g4622.t2 exon g4622.t2.exon5 3659841 3660327
chr_2 g4622 g4622.t2 cds g4622.t2.CDS5 3659841 3660045
chr_2 g4622 g4622.t2 TSS g4622.t2 NA NA

Sequences

>g4622.t2 Gene=g4622 Length=1275
ATGTCTCTTGATTTTGGTATGTAGTAAAATTAATGTTAGGAATTTTTTCAGAATACAATT
CAAACTCCTTTTGGTAATGCCTTTCGTTAATTTAACTTGACTCATAAAAATTTATTACAG
ATCAATACTTTTAATTAAAAACTTTTAAATGTCTTAGTTTATGAGTCAATAACATTTATA
AATTTTCATCTGTATCAATAAAGTGTCAAAATATATTGTCAATGCTCATCTCATAAGTAA
TTTATTTGTATCAAAGAAGTAGTCATTATAAGAAGTTCAAAAATGTTCTACTCTTATATT
TTATTTTTAATAAATTATCTCTTTTTAATAATTTATTATTTTTTAATATTTGTTGGTGTA
GCAAATTTTTGTTATTATTTGTGCCATTGTTTAAAATCACCACTTGATATAACTTTGAAT
ATTTTAAAATCTTTATTTTTTTCATCAGAAAGAAAAAGTTTTAGTGAAAAATATGGTGAA
TGGGCAGTGATAACTGGATCATCTGATGGAATTGGCAAGCAATATGCAAAAGAATTAGCA
AAGAAAGGAATGAAAATTGTTTTGATTTCAAATGTTGAAAAAGATTTGATCAAAGTTAAA
GAAGAAATTGAACAAGAACATTCAGTAGAAGTAAAATATATTTTTGCAGACTTCAGTAAA
GGAAAAGAAGTTTATGAAGAACTCAAAAAAGAACTTTTATCACTTGATATTGGAATTCTT
ATCAATAATGTTGGAATTTTTCATGAATATCCAAATTATTTTGATTTAATTTCTGAAGAT
TTAATTTGGAAACTTTTAGAAATTAACGTTAAAGCAACAACAATGATGTCAAGAATGATT
ATTCCACAAATGAAGAGCAAGAAACGTGGATTGATCATTAATATTTCATCAGTTATCGCC
ACTTGTCCTATGCCTTTAGCTACTATTTATTCAGCTAGTAAACTTTATGTTCACTTCTTT
ACTTTAGCACTTCGAAAAGAACTCGAAAAATATGGAGTTCAAGTTCAACTTATTTCACCT
TCATTAGTTGCAACTAAAATTAACAGTTTCTCAAAATTCCTAGAAACAAAGAGTTTTATT
ATACCAGACGCAGAAACTTTTGCAAAAAATGCAGTTTTTACTTTTGGTAAAACATCTCAA
ACGACTGGTTATTGGAAACATGCACTTTTGGCGGCTTTTTGTAAATTAGGTTCACAAGCA
ATGAACACATTTTGCTTTCATGAAGTAGGAAAAATAGTCAGAGAAGAATATTTGAGAAAC
AAAAAAACATCATGA

>g4622.t2 Gene=g4622 Length=330
MFYSYILFLINYLFLIIYYFLIFVGVANFCYYLCHCLKSPLDITLNILKSLFFSSERKSF
SEKYGEWAVITGSSDGIGKQYAKELAKKGMKIVLISNVEKDLIKVKEEIEQEHSVEVKYI
FADFSKGKEVYEELKKELLSLDIGILINNVGIFHEYPNYFDLISEDLIWKLLEINVKATT
MMSRMIIPQMKSKKRGLIINISSVIATCPMPLATIYSASKLYVHFFTLALRKELEKYGVQ
VQLISPSLVATKINSFSKFLETKSFIIPDAETFAKNAVFTFGKTSQTTGYWKHALLAAFC
KLGSQAMNTFCFHEVGKIVREEYLRNKKTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4622.t2 CDD cd05356 17beta-HSD1_like_SDR_c 65 302 1.8393E-101
13 g4622.t2 Gene3D G3DSA:3.40.50.720 - 59 300 2.2E-49
2 g4622.t2 PANTHER PTHR43899:SF9 MIP25013P-RELATED 16 328 4.6E-110
3 g4622.t2 PANTHER PTHR43899 RH59310P 16 328 4.6E-110
19 g4622.t2 PIRSF PIRSF000126 11-beta-HSD1 17 326 3.8E-95
9 g4622.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 67 84 1.4E-18
4 g4622.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 141 152 4.9E-8
8 g4622.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 141 152 1.4E-18
7 g4622.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 190 206 1.4E-18
5 g4622.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 196 204 4.9E-8
6 g4622.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 216 235 4.9E-8
11 g4622.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 216 235 1.4E-18
10 g4622.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 237 254 1.4E-18
1 g4622.t2 Pfam PF00106 short chain dehydrogenase 67 255 1.2E-44
15 g4622.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g4622.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 34 -
14 g4622.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 35 196 -
17 g4622.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 197 218 -
16 g4622.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 219 330 -
23 g4622.t2 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 203 231 -
12 g4622.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 65 298 1.24E-46
22 g4622.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
21 g4622.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

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. There were no conditions that were differentially expressed