General information for g17558.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Inhibin beta chain.
Parent gene
- The parent gene g17558 is located on chr_4: 13864877..13873914 (- 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 | g17558 | g17558.t1 | isoform | g17558.t1 | 13864877 | 13873914 |
| chr_4 | g17558 | g17558.t1 | exon | g17558.t1.exon1 | 13864877 | 13865524 |
| chr_4 | g17558 | g17558.t1 | cds | g17558.t1.CDS1 | 13864877 | 13865524 |
| chr_4 | g17558 | g17558.t1 | exon | g17558.t1.exon2 | 13865668 | 13866323 |
| chr_4 | g17558 | g17558.t1 | cds | g17558.t1.CDS2 | 13865668 | 13866323 |
| chr_4 | g17558 | g17558.t1 | exon | g17558.t1.exon3 | 13873233 | 13873914 |
| chr_4 | g17558 | g17558.t1 | cds | g17558.t1.CDS3 | 13873233 | 13873914 |
| chr_4 | g17558 | g17558.t1 | TSS | g17558.t1 | NA | NA |
| chr_4 | g17558 | g17558.t1 | TTS | g17558.t1 | NA | NA |
Sequences
>g17558.t1 Gene=g17558 Length=1986
ATGTCGCTTGGTTTCAATTGTAAATTAAGAGAATTTCTTTTGCCACTGCTCATCAGTCTC
ATTTTCATACACATTGTTGTGGCTGATGATGTAGAAGAAGAGCTAAGAAAAGCTCAGAAA
TTGAAATTTCAACAAAAAGAACAGCTATTATTACAAATGCAGCACGAAATTCAAGTTCAG
CTGCAAAATTTATATAATGAGCAGCATCAGCAAGGCAATGATCAAATTGGTAGTTATGAA
TATCCATCATATTGTGCAAATTGTCTTGGTGATACATTCGAACCAGCTAGTAAAAATTTA
CTTAGTTCAGAATTTTCACGTGTCAACGATGATGAAACAAAAACTTCACAAAGTGAAAGC
GAATTTAATCAGTTGAGTGACCATAGAAGACTTGAAGCAATTAAACAACAAATCCTGCTA
AAACTCAATCTTCGTGAGAAACCAAATATTACAAATTCTATACCTAAACAATTAGTACTA
GATACACTAAATCATGCAGAAGAGCGAGAGTTTGGTTTTATGCAGATGCAAATGATGCAG
TCAAGTGATTCAATTGTCGAAAAACTGCAATCATTAAAAACAAAAGCATCAAATGAAAGC
ACTCCTAATAGTGATGAGGATGACAACGATTTTGATGATTTTTATGGAAAGACTAGAGAA
ATTATAATATTTGCAGAAAAAGGTCATCGCATTAATAATCATCACATCTTGTCATTCTCG
ACGGCAATCGATAATCAGCCAGATGCGAAGCTCAAAATTCGCATGGCAACACTATGGCTG
ATGGTAAAGAGACAACCACTTATGCAGAGTCCTACGAAAAGAAGTAAACGTGGTAGTCAG
CATGTAAATAAAGTAAATCAAATGAAAAACCAAAAATTCGACCACAAAAGACGAAAACGA
AGGAGAAAAGAGCATCATGGACCGAGTGACGGTTACGACAACGATAAGACGAATAACAAT
AATTTAGAGTATTTTTATTATGAAAATCATAGTTTTAACAACCATATCACTAATGATAAT
AATAATAATGATAATCATATCATTAAAAGTAATAGTTACGACGATGAGCAATGGCATGAT
GGTGGTGGTGAAGCTGTCGAAAATGACACGCTCTTGAGAAGTCTGAGTAGTGCGGAATAC
AAAAAGTTTGCCTATTTCACACAGTTTCATAACAAAAGCCATGAACAAAATGCCTCCACG
AATCAAAACGATGATATTGATAATAAAACTTATAGACATAAGCATATGAGACATAATGTT
ACACTGTGGATATTTCGTGTACACGACACTAATCTTAGTGACTATAATAGCGCTGTGGAT
TATGATTTTACTGATGAGAAACTTCGAGATCGAATAGAATTCAGTGTATCAAAAGAAATT
ACACTTTCAAAACTTGGCTGGAATAAGGTCGATGTGACATCATTACTTAAGAAATGGTAT
GCTGAACATTACAGTAAAGTGACTTTAGTAGGTAATAAAGAATCACGACTGCAGTTATTC
ATTGACTGCACAGGTTGTGTGAGAAACCATTTGCAAGTTCAATTATTAAATGATAAAAAT
CTTTCTGAAAATGAACAAAATAAACCATTCCTAGTAGTAAACATAGAACCAAATATTGTG
CGGAGAACGCGAAGGCGTGCCATCGATTGTTCTAATGCAGGCAGAAGTCAGTGTTGCAAA
CAGCGATTTTATGTGAGTTTTAAGACACTAGGATGGGATGATTGGATTATTGCACCACCT
GGCTATTATGCAAATTATTGTAGAGGTGATTGTGGTAATGGTATTCATCGGACGCCTGAT
ACTCTTCTCACCTATTATTCGCATGTGTTTCATGAGGTACGAAAATATAGTAAACTTAAT
GGAAATCAACTTTGTTGTGCACCATTGAAATATTCAAGCATGTCACTGATATATTTCGGA
CCTGATGGAAAAATCATTAAACGCGATTTACCAAAAATGGTAGTTGATGAATGTGGATGT
CCGTGA
>g17558.t1 Gene=g17558 Length=661
MSLGFNCKLREFLLPLLISLIFIHIVVADDVEEELRKAQKLKFQQKEQLLLQMQHEIQVQ
LQNLYNEQHQQGNDQIGSYEYPSYCANCLGDTFEPASKNLLSSEFSRVNDDETKTSQSES
EFNQLSDHRRLEAIKQQILLKLNLREKPNITNSIPKQLVLDTLNHAEEREFGFMQMQMMQ
SSDSIVEKLQSLKTKASNESTPNSDEDDNDFDDFYGKTREIIIFAEKGHRINNHHILSFS
TAIDNQPDAKLKIRMATLWLMVKRQPLMQSPTKRSKRGSQHVNKVNQMKNQKFDHKRRKR
RRKEHHGPSDGYDNDKTNNNNLEYFYYENHSFNNHITNDNNNNDNHIIKSNSYDDEQWHD
GGGEAVENDTLLRSLSSAEYKKFAYFTQFHNKSHEQNASTNQNDDIDNKTYRHKHMRHNV
TLWIFRVHDTNLSDYNSAVDYDFTDEKLRDRIEFSVSKEITLSKLGWNKVDVTSLLKKWY
AEHYSKVTLVGNKESRLQLFIDCTGCVRNHLQVQLLNDKNLSENEQNKPFLVVNIEPNIV
RRTRRRAIDCSNAGRSQCCKQRFYVSFKTLGWDDWIIAPPGYYANYCRGDCGNGIHRTPD
TLLTYYSHVFHEVRKYSKLNGNQLCCAPLKYSSMSLIYFGPDGKIIKRDLPKMVVDECGC
P
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g17558.t1 | CDD | cd13752 | TGF_beta_INHB | 558 | 660 | 1.91856E-46 |
| 7 | g17558.t1 | Coils | Coil | Coil | 28 | 48 | - |
| 6 | g17558.t1 | Gene3D | G3DSA:2.10.90.10 | - | 547 | 660 | 5.0E-35 |
| 17 | g17558.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 317 | - |
| 18 | g17558.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 268 | 287 | - |
| 16 | g17558.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 291 | 305 | - |
| 2 | g17558.t1 | PANTHER | PTHR11848:SF178 | INHIBIN BETA CHAIN | 117 | 661 | 4.3E-73 |
| 3 | g17558.t1 | PANTHER | PTHR11848 | TGF-BETA FAMILY | 117 | 661 | 4.3E-73 |
| 1 | g17558.t1 | Pfam | PF00019 | Transforming growth factor beta like domain | 557 | 660 | 4.2E-27 |
| 9 | g17558.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 28 | - |
| 10 | g17558.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 11 | - |
| 11 | g17558.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 12 | 23 | - |
| 12 | g17558.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 24 | 28 | - |
| 8 | g17558.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 29 | 661 | - |
| 15 | g17558.t1 | ProSitePatterns | PS00250 | TGF-beta family signature. | 576 | 591 | - |
| 19 | g17558.t1 | ProSiteProfiles | PS51362 | TGF-beta family profile. | 542 | 661 | 31.649 |
| 14 | g17558.t1 | SMART | SM00204 | TGFB_2 | 558 | 661 | 1.3E-34 |
| 4 | g17558.t1 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 551 | 660 | 2.45E-30 |
| 5 | g17558.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 28 | - |
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:0008083 | growth factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K22687 (inhibin beta B chain)
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