General information for g15714.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cyclic nucleotide-gated cation channel beta-1.
Parent gene
- The parent gene g15714 is located on chr_4: 6504440..6510017 (- 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 | g15714 | g15714.t1 | isoform | g15714.t1 | 6504440 | 6510017 |
| chr_4 | g15714 | g15714.t1 | exon | g15714.t1.exon1 | 6504440 | 6505402 |
| chr_4 | g15714 | g15714.t1 | cds | g15714.t1.CDS1 | 6504440 | 6505402 |
| chr_4 | g15714 | g15714.t1 | exon | g15714.t1.exon2 | 6507964 | 6508184 |
| chr_4 | g15714 | g15714.t1 | cds | g15714.t1.CDS2 | 6507964 | 6508184 |
| chr_4 | g15714 | g15714.t1 | exon | g15714.t1.exon3 | 6508313 | 6509241 |
| chr_4 | g15714 | g15714.t1 | cds | g15714.t1.CDS3 | 6508313 | 6509241 |
| chr_4 | g15714 | g15714.t1 | exon | g15714.t1.exon4 | 6509335 | 6510017 |
| chr_4 | g15714 | g15714.t1 | cds | g15714.t1.CDS4 | 6509335 | 6510017 |
| chr_4 | g15714 | g15714.t1 | TSS | g15714.t1 | 6510383 | 6510383 |
| chr_4 | g15714 | g15714.t1 | TTS | g15714.t1 | NA | NA |
Sequences
>g15714.t1 Gene=g15714 Length=2796
ATGACATCACAAGCTTCACTTTTATCATCACCAGACAATTCAGTAAAATATCGTTCAAAT
TCTCGTTCTGCTTCGAATTCAAATCTTTACAAATCACTCGAGGATATTCAAAAAAACCTT
GACAGTCTTGATAATTTTCTAACGATAACTGAAGACATTTTGACAAGAGAACGATATCAT
GATATGGAGCTTTATAAACGAGAAAGAGAACGAAAAAATACAGGAGGAAAACTTCTTGAA
TCACCAGCATCAACTTGTCATCCACCGCCATTATCTTTTAAAAATGGAAAAATTTTCTGT
CCAGCTGTAACCGCGACTTTCAATCCATCAAATGTTCAATTAAATTTCGAAATTGTCAAG
CAAATTATCAACAATCAGAATAATTTTTTATGCTATGACAATCACGAAATGGATGAACAA
GAAATAGCATCATCATCACCTGATGTAAATTTGTCAGATGAACAAGATATTTTTATGACA
CATAAAGAAGATGATGAAGAAGTGAAATTGAAATCAATGAATAATTTATTGATGAAATCA
AATTCAACAATCAGTAGCAAATTGGATGATGCAGTGATGAAAAGTATTGAAGATGAAATT
ATTGAATATGAAAGAGATATGAGGGAAAATTATGAAAAAAGTGAAACTATGGAATGCATG
ATTTTACCACCTGAAACTCCTGAAAAATCTCAACTCACACAATCGACATCAATTTCGCAT
CAATCTTCATCTCCAACACCTAGTGAAAAGCCAATTACAAATCGGTTTATTCAGCATTCA
TTTCGTAATCTTATCCACAAATTTAATGAACGTTCACGGCGTATGCAAAATCGACTTAAA
CGTCCACCATCACCAACTTCAAGTGGTAGTGTATCAACATCAACACCATTGCATATGAAA
TTACTTTATGGAGTAAAAAATGATGATAATGATGATGTTGTGGTTGTTGAAGAAGGAACT
GACACTGATGGTCATTTGGCAGGACGACAAAAGCGACCGTTAGCACAAATCGCAATTGAA
TCACCAGCTGCACTTGAAAAAGAAGATCCAAATGTTCACAATCAATGTTCTATATTTTGT
TGCTGTAATGGACCAGTTTTAGATCCACAAGGAAAATTTTACATTTCATGGCTTTTCATT
GTGACACTTTCATTTCTATATAATGCTTTTGTTATTCCACTTCGTACGTCTTTTCCATTT
CAAACTGTTGATAATCAACATTTATGGCTAACAATGGACATTGTGGTTGATGTTGTTTAT
TTAGTTGACTTGTTGTTCATCAAACATCGAAAAATGTATCTTTTTGAAGGCTTTTGGGTT
AAAGATCGACAATTGACAAGGAAAAATTACATGAGAAAACTTCAATTTAAAATGGATGTT
GTTTCCTTGCTACCACTTGATATTCTTTATTTTATACCATGGTTTGGACGAAGTGCAGTT
TACTTAAGAGTTCCAAGATTGCTAAAAATTCAAAGCTTTTGGGAATTTTTTAAACTTCTC
GATCGTGTCATTGCTTCACCGCATATTTTAAGAGTTATTAAGACATTGAGCTATATGCTT
TATATGATTCACTTGACTGCTTGTACTTATTATGCTGTCAGCTTTTATAAAGGACTTGGC
ATAAATCGATGGGTATTCAGTGGTAAAGGTCATCCATATGTGCGATGTTTTGCTTTTGCA
ACAAAAACAGCAACGTCAATTGGCAAAAATCCAAAACCATCTGAAGTTGATGAATATTTA
TTTATGACTTGTGCATGGTTGATGGGAGTTTTTGTATTTGCATTATTGATTGGTCAGATT
AGAGATATCATATCAACAGCTACAAGGTCACAGAGCGAATACAAACAGCTTGTTGATGAA
ACTCTCGAATACATGCGTCGCTTACAACTTCCAACTGAACTTCAACGTCGTGTCAAACAA
TGGTTTACTTTTACATGGGACCAACAACGAAGTCTTGATGAATCACACATTCTTGATTCA
CTTCCAGCTAATCTCAAAACAGACATTGCCATTTCAGTACACATTCAAACTTTATCAAAA
GTTCAACTTTTTTCAGGATGTGATGAAGCTTTTCTTCGTGAACTTGTTCTAAAATTGCGC
TCTGTAATTTTTTTACCTATGGATTATGTCTGCAAAAAAGGTGAAGTTGGCAAAGAAATG
TACATTATAAAAACAGGCAAAATTGAAGTTTTAGGCAAGAATGATGAAGTTTTAGCAACT
CTCTGTACTGGTGCATGCTTTGGTGAAATTTCTTTGCTTGATATTAGTGGCGGACCACAA
GGAAATAGAAGAACTGCAGATGTTAGATCAAAAGGTTTTTCAAATCTCTTTGTGCTATCA
AAATCTGATCTCGAAGAAGTCATTGTTCATTATGAAGATGCAAGAGCAGCATTAGAAAGT
CGAGCAAAAGCTTTATTGAAAGAAAATGCAAATCGTGATAAACGAGAAGCAAAATTGCGA
AGACCAAGCATGTTATCAGTGAAATCTGAAGAAGAAGTTGTCATTGATAATCCAAAAACA
CCAAATCAACCTAAATTACTCGATGCAGTCATTCAAGCTTTGCCTTCAAATTCACCAGCT
GCACAGTTATTGACTAGAGGTTCACGGAAGGGCAAAAAACGAGTTGGACCAGCACCAGCC
GATTTTAAAATTGAAAATGAAATTGTTAAAGAAAATATGAATTTGACTGATAGTGAAAAA
GAATTGATGATGAGAGTAAATGAAAATGGAAAAAGTGTAAAATGTGATGTGCATAAGGAA
ATGGATGTTGATGATGCTAAGAAAAAAGAAGATTAA
>g15714.t1 Gene=g15714 Length=931
MTSQASLLSSPDNSVKYRSNSRSASNSNLYKSLEDIQKNLDSLDNFLTITEDILTRERYH
DMELYKRERERKNTGGKLLESPASTCHPPPLSFKNGKIFCPAVTATFNPSNVQLNFEIVK
QIINNQNNFLCYDNHEMDEQEIASSSPDVNLSDEQDIFMTHKEDDEEVKLKSMNNLLMKS
NSTISSKLDDAVMKSIEDEIIEYERDMRENYEKSETMECMILPPETPEKSQLTQSTSISH
QSSSPTPSEKPITNRFIQHSFRNLIHKFNERSRRMQNRLKRPPSPTSSGSVSTSTPLHMK
LLYGVKNDDNDDVVVVEEGTDTDGHLAGRQKRPLAQIAIESPAALEKEDPNVHNQCSIFC
CCNGPVLDPQGKFYISWLFIVTLSFLYNAFVIPLRTSFPFQTVDNQHLWLTMDIVVDVVY
LVDLLFIKHRKMYLFEGFWVKDRQLTRKNYMRKLQFKMDVVSLLPLDILYFIPWFGRSAV
YLRVPRLLKIQSFWEFFKLLDRVIASPHILRVIKTLSYMLYMIHLTACTYYAVSFYKGLG
INRWVFSGKGHPYVRCFAFATKTATSIGKNPKPSEVDEYLFMTCAWLMGVFVFALLIGQI
RDIISTATRSQSEYKQLVDETLEYMRRLQLPTELQRRVKQWFTFTWDQQRSLDESHILDS
LPANLKTDIAISVHIQTLSKVQLFSGCDEAFLRELVLKLRSVIFLPMDYVCKKGEVGKEM
YIIKTGKIEVLGKNDEVLATLCTGACFGEISLLDISGGPQGNRRTADVRSKGFSNLFVLS
KSDLEEVIVHYEDARAALESRAKALLKENANRDKREAKLRRPSMLSVKSEEEVVIDNPKT
PNQPKLLDAVIQALPSNSPAAQLLTRGSRKGKKRVGPAPADFKIENEIVKENMNLTDSEK
ELMMRVNENGKSVKCDVHKEMDVDDAKKKED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g15714.t1 | CDD | cd00038 | CAP_ED | 683 | 798 | 5.18579E-23 |
| 10 | g15714.t1 | Coils | Coil | Coil | 193 | 213 | - |
| 9 | g15714.t1 | Coils | Coil | Coil | 781 | 808 | - |
| 11 | g15714.t1 | Coils | Coil | Coil | 921 | 931 | - |
| 7 | g15714.t1 | Gene3D | G3DSA:1.10.287.630 | Helix hairpin bin | 609 | 674 | 5.5E-18 |
| 8 | g15714.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 676 | 808 | 9.6E-35 |
| 35 | g15714.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 36 | g15714.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 252 | - |
| 33 | g15714.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 252 | - |
| 34 | g15714.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 293 | - |
| 32 | g15714.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 279 | 293 | - |
| 3 | g15714.t1 | PANTHER | PTHR45638 | CYCLIC NUCLEOTIDE-GATED CATION CHANNEL SUBUNIT A | 37 | 912 | 5.6E-290 |
| 4 | g15714.t1 | PANTHER | PTHR45638:SF1 | CYCLIC NUCLEOTIDE-GATED ION CHANNEL SUBUNIT B, ISOFORM A | 37 | 912 | 5.6E-290 |
| 1 | g15714.t1 | Pfam | PF00520 | Ion transport protein | 376 | 610 | 2.0E-17 |
| 2 | g15714.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 704 | 788 | 1.9E-14 |
| 12 | g15714.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 372 | - |
| 18 | g15714.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 373 | 394 | - |
| 15 | g15714.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 395 | 405 | - |
| 21 | g15714.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 427 | - |
| 13 | g15714.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 428 | 455 | - |
| 22 | g15714.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 456 | 476 | - |
| 17 | g15714.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 477 | 517 | - |
| 20 | g15714.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 518 | 539 | - |
| 14 | g15714.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 540 | 578 | - |
| 19 | g15714.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 600 | - |
| 16 | g15714.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 601 | 931 | - |
| 31 | g15714.t1 | ProSitePatterns | PS00888 | Cyclic nucleotide-binding domain signature 1. | 710 | 726 | - |
| 30 | g15714.t1 | ProSitePatterns | PS00889 | Cyclic nucleotide-binding domain signature 2. | 747 | 770 | - |
| 37 | g15714.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 683 | 788 | 22.844 |
| 29 | g15714.t1 | SMART | SM00100 | cnmp_10 | 683 | 803 | 4.7E-20 |
| 5 | g15714.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 368 | 605 | 3.01E-21 |
| 6 | g15714.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 609 | 797 | 5.24E-45 |
| 28 | g15714.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 373 | 395 | - |
| 26 | g15714.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 408 | 427 | - |
| 25 | g15714.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 482 | - |
| 24 | g15714.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 520 | 542 | - |
| 27 | g15714.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 598 | - |
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:0016020 | membrane | CC |
| GO:0055085 | transmembrane transport | BP |
| GO:0005216 | ion channel activity | MF |
| GO:0006811 | ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04952 (cyclic nucleotide gated channel beta 1)
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