General information for g6880.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 3 beta-hydroxysteroid dehydrogenase/Delta 5–>4-isomerase type 4.
Parent gene
- The parent gene g6880 is located on chr_2: 19630416..19650421 (- strand)
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 | g6880 | g6880.t1 | TTS | g6880.t1 | 19630254 | 19630254 |
| chr_2 | g6880 | g6880.t1 | isoform | g6880.t1 | 19630416 | 19650421 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon1 | 19630416 | 19630864 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS1 | 19630416 | 19630864 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon2 | 19631398 | 19631547 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS2 | 19631398 | 19631547 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon3 | 19634365 | 19634537 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS3 | 19634365 | 19634537 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon4 | 19635171 | 19635249 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS4 | 19635171 | 19635249 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon5 | 19638662 | 19638826 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS5 | 19638662 | 19638826 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon6 | 19638883 | 19638990 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS6 | 19638883 | 19638990 |
| chr_2 | g6880 | g6880.t1 | exon | g6880.t1.exon7 | 19650382 | 19650421 |
| chr_2 | g6880 | g6880.t1 | cds | g6880.t1.CDS7 | 19650382 | 19650421 |
| chr_2 | g6880 | g6880.t1 | TSS | g6880.t1 | NA | NA |
Sequences
>g6880.t1 Gene=g6880 Length=1164
ATGTCAGCTGAAACTGCTAATGATGTCATTTTAATTACCGGTGGCAGTGGATTTTTAGGG
CAGCATATTGTACGACTGATTGAGGAGCGTGATCTAACAGTAAAGGAAATTCGTATTGTG
GACTTGCGACCATACGAAAATCGATTAAACCATTCAGAAAAGATCAAACTTGTTAGCATT
GTTGGTGATATTTGTGATCCATTGAGTATTGAATATGCTTTTGAGGGCGTTGACTGTGTT
TTTCATTGCGCTGCCAACATTAATTTCCAATTTCCAACAGCAACTGATGAGTTAGAGCGT
GTCAATGTGACGGGCACACAGAACATAATTGATCTCTGCATCAAATACAATGTGCCGAAT
CTAATCTACACGAGCACTGCATTGGTAACATTTATTCCATGCATGGGTAAAGGGACATTT
TCGATAATAGTGAATCAAACAGAGAATAAAGCAAAAGCAGCTTCATGCGATAGTCAATTT
CTCATTCCTGGCTTTCCAGCTTCTAAATTGCGAGCCGAGAAGTTTGTGTTGTCATCGTAT
GGCCGAAAGTTGAGCAATGGAAAAGGACATTTGAAAACAGTGAGTTTGCGACCAACTTTG
ATGTATGGTGAAGAAGATCAACGATTCTTTCCAACTATAATGCGGTTTGCAGATCGATGG
AATGGTCGAATCCCGAGGATTGCAGAGACTGGAAAGAAACAGATCACATATGTTGGCAAT
GTGGCGTGGGCTCATCTCTGTGCAATGGAGAAATTGAAAAACGAGCCAAAGAATATAGTA
GGAATCCCCATTTTCATAACCGATGACAGTCCTATCACAGATACCGTAAGATTAACTCAA
CGTATCAATGTTGACATGGAGACATTTAAAATAAAACCCACATCATGGTCCATTCCATAT
TTATTGTGTTATCTTATCGCAATGATTATAGAGGTGTTCATTAAAGTCATCAATTTGTTT
ACGAATTATCATATTGAATATTGTCCATGCGGTATGTTAGCTGCTGCAGCATCATTTGTG
TTTTACGATCGACTACGAAGCTCAATTGCACTCGAGTATGAGCCAATTTATAGTGTTAAT
GAAGGATTTTCTAGAAGTGCAAAATGGTATGATTTGTGGTATCAACAATATAAGGATAAA
AAGCTTAAGGAAAAACAACAATGA
>g6880.t1 Gene=g6880 Length=387
MSAETANDVILITGGSGFLGQHIVRLIEERDLTVKEIRIVDLRPYENRLNHSEKIKLVSI
VGDICDPLSIEYAFEGVDCVFHCAANINFQFPTATDELERVNVTGTQNIIDLCIKYNVPN
LIYTSTALVTFIPCMGKGTFSIIVNQTENKAKAASCDSQFLIPGFPASKLRAEKFVLSSY
GRKLSNGKGHLKTVSLRPTLMYGEEDQRFFPTIMRFADRWNGRIPRIAETGKKQITYVGN
VAWAHLCAMEKLKNEPKNIVGIPIFITDDSPITDTVRLTQRINVDMETFKIKPTSWSIPY
LLCYLIAMIIEVFIKVINLFTNYHIEYCPCGMLAAAASFVFYDRLRSSIALEYEPIYSVN
EGFSRSAKWYDLWYQQYKDKKLKEKQQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6880.t1 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 373 | 1.2E-57 |
| 2 | g6880.t1 | PANTHER | PTHR10366:SF637 | HYDROXYSTEROID DEHYDROGENASE, PUTATIVE-RELATED | 6 | 371 | 4.0E-69 |
| 3 | g6880.t1 | PANTHER | PTHR10366 | NAD DEPENDENT EPIMERASE/DEHYDRATASE | 6 | 371 | 4.0E-69 |
| 1 | g6880.t1 | Pfam | PF01073 | 3-beta hydroxysteroid dehydrogenase/isomerase family | 11 | 282 | 2.4E-57 |
| 8 | g6880.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 297 | - |
| 11 | g6880.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 317 | - |
| 9 | g6880.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 318 | 322 | - |
| 10 | g6880.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 342 | - |
| 7 | g6880.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 343 | 387 | - |
| 5 | g6880.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 8 | 371 | 1.22E-42 |
| 4 | g6880.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 320 | - |
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:0006694 | steroid biosynthetic process | BP |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | MF |
| GO:0003854 | 3-beta-hydroxy-delta5-steroid dehydrogenase activity | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K00070 (3beta-hydroxy-Delta5-steroid dehydrogenase / steroid Delta-isomerase)
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