General information for g15718.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g15718 is located on chr_4: 6537911..6538572 (- 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_4 | g15718 | g15718.t1 | TTS | g15718.t1 | 6537839 | 6537839 |
| chr_4 | g15718 | g15718.t1 | isoform | g15718.t1 | 6537911 | 6538572 |
| chr_4 | g15718 | g15718.t1 | exon | g15718.t1.exon1 | 6537911 | 6538344 |
| chr_4 | g15718 | g15718.t1 | cds | g15718.t1.CDS1 | 6537911 | 6538344 |
| chr_4 | g15718 | g15718.t1 | exon | g15718.t1.exon2 | 6538401 | 6538489 |
| chr_4 | g15718 | g15718.t1 | cds | g15718.t1.CDS2 | 6538401 | 6538489 |
| chr_4 | g15718 | g15718.t1 | exon | g15718.t1.exon3 | 6538559 | 6538572 |
| chr_4 | g15718 | g15718.t1 | cds | g15718.t1.CDS3 | 6538559 | 6538572 |
| chr_4 | g15718 | g15718.t1 | TSS | g15718.t1 | 6538647 | 6538647 |
Sequences
>g15718.t1 Gene=g15718 Length=537
ATGGGGAATTATTTTGTTCCCATTTTAGTTTTATTTTCTTTATATTTTGCATCGTGTATT
TCTACTGAATTTCCTGCAATTATTGAACAAGAAAAAATAATTGCACCAATAGGATGTCAT
AGAAGACTCTACACATTTCAAGTGACTCAAACAGACTCGAAAGGATATGTATGTAGTGAA
AAAGTTACAGTAAATGCCTGCTATGGTCGTTGTGATAGCAAAGAAATAAGTGATTGGAAA
TTTCCTTTCAAAAGATCCTACCATCCTGTTTGTGTCCCAAAAGGAATAACAAAAGTTGTA
ATTATGCTTGAAAATTGCGATCCTGAAGCTGGCTTAGAAGCTAGACGTTATGAATATCTT
GAACCACTCTCTTGTAATTGCCAAATTTGCTCATCAATTAATACTTCCTGTGAATCACCA
CAATTATTGCATAAAAATCATCAACAAGTTGCTGGTGGAAAATCATCTGCATCAGTTCCA
ATTTTTGATGGAACTTTTATTGATGACAATGAAAATTTTATTGCAAATAATAAGTAA
>g15718.t1 Gene=g15718 Length=178
MGNYFVPILVLFSLYFASCISTEFPAIIEQEKIIAPIGCHRRLYTFQVTQTDSKGYVCSE
KVTVNACYGRCDSKEISDWKFPFKRSYHPVCVPKGITKVVIMLENCDPEAGLEARRYEYL
EPLSCNCQICSSINTSCESPQLLHKNHQQVAGGKSSASVPIFDGTFIDDNENFIANNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g15718.t1 | CDD | cd00069 | GHB_like | 39 | 138 | 1.28774E-26 |
| 6 | g15718.t1 | Gene3D | G3DSA:2.10.90.10 | - | 32 | 147 | 1.9E-9 |
| 2 | g15718.t1 | PANTHER | PTHR11515 | GLYCOPROTEIN HORMONE BETA CHAIN | 21 | 141 | 9.7E-32 |
| 3 | g15718.t1 | PANTHER | PTHR11515:SF13 | GLYCOPROTEIN HORMONE BETA 5, ISOFORM A | 21 | 141 | 9.7E-32 |
| 1 | g15718.t1 | Pfam | PF00007 | Cystine-knot domain | 39 | 142 | 5.5E-6 |
| 8 | g15718.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 9 | g15718.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 10 | g15718.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 16 | - |
| 11 | g15718.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 7 | g15718.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 178 | - |
| 4 | g15718.t1 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 35 | 140 | 3.51E-17 |
| 5 | g15718.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 13 | g15718.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
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:0005576 | extracellular region | CC |
| GO:0005179 | hormone activity | MF |
KEGG
Orthology
- This transcript has been annotated with K25484 (glycoprotein hormone beta-5)
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