General information for g16533.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lutropin-choriogonadotropic hormone receptor.
Parent gene
- The parent gene g16533 is located on chr_4: 9812704..9819027 (- 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 | g16533 | g16533.t1 | isoform | g16533.t1 | 9812704 | 9819027 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon1 | 9812704 | 9812943 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS1 | 9812704 | 9812943 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon2 | 9813000 | 9813119 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS2 | 9813000 | 9813119 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon3 | 9813177 | 9813369 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS3 | 9813177 | 9813369 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon4 | 9814085 | 9814313 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS4 | 9814085 | 9814313 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon5 | 9814383 | 9814583 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS5 | 9814383 | 9814583 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon6 | 9815651 | 9815748 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS6 | 9815651 | 9815748 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon7 | 9815951 | 9816276 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS7 | 9815951 | 9816276 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon8 | 9816347 | 9816464 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS8 | 9816347 | 9816464 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon9 | 9816889 | 9816963 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS9 | 9816889 | 9816963 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon10 | 9817073 | 9817141 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS10 | 9817073 | 9817141 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon11 | 9817223 | 9817288 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS11 | 9817223 | 9817288 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon12 | 9817409 | 9817483 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS12 | 9817409 | 9817483 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon13 | 9817910 | 9817987 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS13 | 9817910 | 9817987 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon14 | 9818134 | 9818208 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS14 | 9818134 | 9818208 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon15 | 9818441 | 9818589 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS15 | 9818441 | 9818589 |
| chr_4 | g16533 | g16533.t1 | exon | g16533.t1.exon16 | 9818863 | 9819027 |
| chr_4 | g16533 | g16533.t1 | cds | g16533.t1.CDS16 | 9818863 | 9819027 |
| chr_4 | g16533 | g16533.t1 | TSS | g16533.t1 | NA | NA |
| chr_4 | g16533 | g16533.t1 | TTS | g16533.t1 | NA | NA |
Sequences
>g16533.t1 Gene=g16533 Length=2277
ATGTTTGGGTTGATTTTCGTATTGCTCGCTTTGCTGACGACGACGCTCGAAGCGAGAAAC
TCAAATTTCGCATTTGTTGAAAATTTTCATCCGGGATTGAATGACATTAGTAGGCGAAAT
TATACATCATGGTGCTCCTGCTCAAATGACCTTATCGATACGATTGGTGAATCAGAATGT
CATTGTGAAGGACAAAATTTACTTGCCATACCAAAAAATTTACACAATGTAACAAGACTT
TCAATTGCAAACGCTAATATTAAAGAAATTGTACAAAAAGGACTGAATAGATATTCCATT
TCATTGAGAGATGTAATCTTAACTAATCTTAAGGAATTTAATTACATAGAGCCGTATGTT
TTTCGTGATGTGATAAATTTGAGAACCATATACATTTCTTATTCACCAAAATTGGAACAA
ATTTCTGCCGAAGCCTTCTATCATTCATCTAAAAGCTTTAAAATGCTGAAAATTATGAAT
TCAGGCTTGAAAGAAGTTCCAAATATGAAGTATTTATCAAATTGTGATATTCTTTCGCAA
GTAGATTTTGAAGGGAATTTTATTACGGAAATTCATGAGAATTCAATTCGCATCAAGACA
GAAGAATTAAATTTAGACAATAATTTCATAACAACTGTACAGAGAGCAGCTTTTAATGGA
TCAGCTATAGGAAAGCTAAGCCTTAAAGGAAATCGGAAATTAAGCAATCTTGATCCACAC
GCTTTTGAAGGAATTTTGAATATTCGAGAATTAGACTTATCAAATACCGCCATTCATTCA
CTCTCAACAAAGGGCTTAGACACGCTCGAGATTCTCCGGATACAAAATACGCACACGCTT
AAACAAATTCCATCTGTTTACAACTTCAAGAGTCTTGAAAAAGCTTTTCTGACACATTCA
TTCCATTGTTGTGCATTCAAGTTTCCTAATCTACATGATCCTATCAGCCACAAACAACAC
CTAGAATTCCTTGAAGGTCTTAAATTTGACTGTCGCGTAAAACGTAAAGCTGAAAATAAA
ATAAATGAAACCGACTTAACTGCAGACTTCTTAGAAAGTCCCGATAAACATTTTGATTAT
TTTGAAAATCTTGGAATTGATCCTGACAATGATATTGATAGAGATGGATTTTTTATGTCA
TCACCTGTCGATCTTGCACAACAAAATGAAGTCATGTGTGGAAAAATTAATATCTTCACA
AGAAACGTTCAATGCCATCCAAAATCAGATGCTCTAAATCCTTGCGAAGATGTAATGGGC
AAAACTTTATGGCTACGTGTTTCTGTATGGATAGTTGTTTCGTTAGCCGTGATTGGCAAT
TCAGCTGTGCTTGTGGTGCTTCTTACAAAACGAGCGGAGTTAACTGTACCTGAATTCTTG
ATGTGCAATTTGGCCTTTGCAGACCTTTGCATGGGAATTTATTTGATGCTCCTTGGTTTC
ATGGATTTATATTCAATGAACGAATATTTTAATTATGCTTATGACTGGCAATATGGTATT
GGTTGTAAAACTGCTGGTTTTTTAACAGTTTTTGCTGTTCATTTGTCAATTTTTACACTC
ACAACAATAACAATTGAGCGATGGTTTGCAATTACAAAAGCAGTTTTTTTAAACAAACGA
CTGAGACATAGGAAGGCAATTTATATTATGATTTGTGGTTGGCTTTATTCAATTGCAATT
GCATTAATGCCTTTGTTTGGTGTCAGCAATTATTCATCAACAAGCATTTGTCTGCCAATG
GAAGCAAAAGATCTCGCAGATATTATTTACTTGACAGTCCTCATGTTATTAAGCGGTTTA
GGATTTTTCATCATAGTCATTTGTTATGTTCAAATTTATTTTAATTTAGGTGATAAAGGA
ATTTCACAACAAAATACAAATAGGGAAATGCTCGTAGCTAAAAAAATGGCACTGCTGGTT
TTTACAAATTTCGCATGTTGGGCACCAATAACATTTTTTGGTGTCTTTGCACTTGTCGGT
CATAGTTTAATTGATGTAAGGAAAGCAAAAATTCTTCTAGTCTTTTTCTATCCACTTAAT
TCCTGTGCAAATCCATATTTATATGCGATACTCACATCACAATATCGTCGTGATGCAATC
TTACTTCTATCAAAATTTGGTTTTTGTTCACAAAGAGTTCAAGAATATAGAAATTATTAT
CGACCACCAAATAATTCAGTTGCATTAAATGTTATGAGTGGAAGTTTAAGCTCATCGCAG
AAAAAATACAGTGATGATAGACGAAATTTACAAAAATTAATTAATGGTGGTTCTTAG
>g16533.t1 Gene=g16533 Length=758
MFGLIFVLLALLTTTLEARNSNFAFVENFHPGLNDISRRNYTSWCSCSNDLIDTIGESEC
HCEGQNLLAIPKNLHNVTRLSIANANIKEIVQKGLNRYSISLRDVILTNLKEFNYIEPYV
FRDVINLRTIYISYSPKLEQISAEAFYHSSKSFKMLKIMNSGLKEVPNMKYLSNCDILSQ
VDFEGNFITEIHENSIRIKTEELNLDNNFITTVQRAAFNGSAIGKLSLKGNRKLSNLDPH
AFEGILNIRELDLSNTAIHSLSTKGLDTLEILRIQNTHTLKQIPSVYNFKSLEKAFLTHS
FHCCAFKFPNLHDPISHKQHLEFLEGLKFDCRVKRKAENKINETDLTADFLESPDKHFDY
FENLGIDPDNDIDRDGFFMSSPVDLAQQNEVMCGKINIFTRNVQCHPKSDALNPCEDVMG
KTLWLRVSVWIVVSLAVIGNSAVLVVLLTKRAELTVPEFLMCNLAFADLCMGIYLMLLGF
MDLYSMNEYFNYAYDWQYGIGCKTAGFLTVFAVHLSIFTLTTITIERWFAITKAVFLNKR
LRHRKAIYIMICGWLYSIAIALMPLFGVSNYSSTSICLPMEAKDLADIIYLTVLMLLSGL
GFFIIVICYVQIYFNLGDKGISQQNTNREMLVAKKMALLVFTNFACWAPITFFGVFALVG
HSLIDVRKAKILLVFFYPLNSCANPYLYAILTSQYRRDAILLLSKFGFCSQRVQEYRNYY
RPPNNSVALNVMSGSLSSSQKKYSDDRRNLQKLINGGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 43 | g16533.t1 | CDD | cd15136 | 7tmA_Glyco_hormone_R | 424 | 698 | 6.69967E-149 |
| 23 | g16533.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 423 | 716 | 6.1E-45 |
| 3 | g16533.t1 | PANTHER | PTHR24372:SF74 | LP13728P | 144 | 748 | 7.0E-181 |
| 4 | g16533.t1 | PANTHER | PTHR24372 | GLYCOPROTEIN HORMONE RECEPTOR | 144 | 748 | 7.0E-181 |
| 18 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 412 | 429 | 2.5E-43 |
| 11 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 424 | 448 | 1.6E-24 |
| 12 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 449 | 462 | 2.5E-43 |
| 10 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 457 | 478 | 1.6E-24 |
| 14 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 489 | 502 | 2.5E-43 |
| 13 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 502 | 516 | 2.5E-43 |
| 7 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 509 | 531 | 1.6E-24 |
| 6 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 545 | 566 | 1.6E-24 |
| 16 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 563 | 574 | 2.5E-43 |
| 9 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 590 | 613 | 1.6E-24 |
| 17 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 628 | 646 | 2.5E-43 |
| 8 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 632 | 656 | 1.6E-24 |
| 15 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 662 | 678 | 2.5E-43 |
| 5 | g16533.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 670 | 696 | 1.6E-24 |
| 19 | g16533.t1 | PRINTS | PR00373 | Glycoprotein hormone receptor signature | 691 | 710 | 2.5E-43 |
| 1 | g16533.t1 | Pfam | PF13855 | Leucine rich repeat | 201 | 258 | 1.4E-9 |
| 2 | g16533.t1 | Pfam | PF00001 | 7 transmembrane receptor (rhodopsin family) | 439 | 688 | 1.8E-36 |
| 32 | g16533.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 33 | g16533.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 34 | g16533.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 42 | g16533.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 28 | g16533.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 422 | - |
| 41 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 423 | 448 | - |
| 26 | g16533.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 449 | 459 | - |
| 35 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 484 | - |
| 31 | g16533.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 485 | 503 | - |
| 37 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 504 | 525 | - |
| 27 | g16533.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 526 | 545 | - |
| 40 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 546 | 568 | - |
| 30 | g16533.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 569 | 587 | - |
| 38 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 616 | - |
| 25 | g16533.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 617 | 636 | - |
| 36 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 637 | 659 | - |
| 29 | g16533.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 660 | 670 | - |
| 39 | g16533.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 671 | 691 | - |
| 24 | g16533.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 692 | 758 | - |
| 52 | g16533.t1 | ProSitePatterns | PS00237 | G-protein coupled receptors family 1 signature. | 515 | 531 | - |
| 53 | g16533.t1 | ProSiteProfiles | PS50262 | G-protein coupled receptors family 1 profile. | 439 | 688 | 31.044 |
| 21 | g16533.t1 | SUPERFAMILY | SSF52058 | L domain-like | 58 | 311 | 1.13E-23 |
| 20 | g16533.t1 | SUPERFAMILY | SSF81321 | Family A G protein-coupled receptor-like | 412 | 717 | 2.93E-55 |
| 22 | g16533.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 44 | g16533.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 51 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 449 | - |
| 45 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 462 | 484 | - |
| 49 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 504 | 526 | - |
| 48 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 546 | 568 | - |
| 50 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 610 | - |
| 46 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 637 | 659 | - |
| 47 | g16533.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 669 | 691 | - |
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:0007186 | G protein-coupled receptor signaling pathway | BP |
| GO:0005515 | protein binding | MF |
| GO:0016500 | protein-hormone receptor activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0004930 | G protein-coupled receptor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04249 (thyrotropin receptor)
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