General information for g4217.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cyclic nucleotide-gated cation channel subunit A.
Parent gene
- The parent gene g4217 is located on chr_2: 296581..312014 (+ 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 | g4217 | g4217.t1 | isoform | g4217.t1 | 296581 | 312014 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon1 | 296581 | 296643 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS1 | 296581 | 296643 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon2 | 296937 | 297167 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS2 | 296937 | 297167 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon3 | 297223 | 297385 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS3 | 297223 | 297385 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon4 | 299449 | 299717 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS4 | 299449 | 299717 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon5 | 300373 | 300478 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS5 | 300373 | 300478 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon6 | 300612 | 300785 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS6 | 300612 | 300785 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon7 | 300859 | 300968 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS7 | 300859 | 300968 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon8 | 303896 | 304301 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS8 | 303896 | 304301 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon9 | 304363 | 304503 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS9 | 304363 | 304503 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon10 | 304579 | 304729 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS10 | 304579 | 304729 |
| chr_2 | g4217 | g4217.t1 | exon | g4217.t1.exon11 | 311825 | 312014 |
| chr_2 | g4217 | g4217.t1 | cds | g4217.t1.CDS11 | 311825 | 312014 |
| chr_2 | g4217 | g4217.t1 | TSS | g4217.t1 | NA | NA |
| chr_2 | g4217 | g4217.t1 | TTS | g4217.t1 | NA | NA |
Sequences
>g4217.t1 Gene=g4217 Length=2004
ATGGTTAAAAAAATTGAAATCGCTGTCATAAGTGCAAACGAAACGAGATGTGATGAAAAA
TTGAATTCATCCAATGACCATTCTTATTCGACATTTCGACGAGCATTGAATGCTTTAAGA
CGTAGAATATCCAGAAAAGAACATCGAACAAGACCGCCAGATAAATTTAATGCAGATAAG
TTTGTGATCACGAATCAAAACGCAATGGGACAGCAGCAGTCAATGAGTGGTAATCCGAGT
GATGGTGTAACTAGTCGACTATCGTTTGATCCGTCCTTGCCGTCATATTACCGGTGGCTC
GCTGTAGTTTCAATAGCTGTGCTATATAACATAATTTTCGTTGTTGGTCGTGCAATATTT
TGGGAGATTAACAAAAAGTCTACATTATTGTGGTATACATTAGACTATTTATGTGATTTT
ATCTACCTGCTCGATACATTAGTGCATGTTCATGAGGGTTACCTCGAGCAAGGTCTTCTT
GTACGTGATGCCAAAAAATTACGCCAACATTACTTTAGCACGAGTCATTGGCGCTTAGAT
GTTTTATCAATGTTACCGACCGACTTTTTCTACTTTTGGTGGGGACCTAATGAATGTAAT
TCTGAAAGAGTTCCATGTGCAGTTATCGTTAGAATTAATCGCCTATTAAGATTACCCCGA
ATGTGGGAATGGTTCGAGCGTACTGAAACTGCAACAGGATATCCGAATGCATTTAGAATA
TGCAAAGTCGTGCTAGCAATATTAGTTTTAATACACTGGAATGCCTGCCTCTATTTTGCC
ATCAGCTATGCTCAAGGCTTTGGCAGCGACAATTGGGTCTATAATTTAAATGGCACTCAA
AATGCTTCGCTAACACGGCAATACATCTATAGCTTTTATTGGTCAACGCTCACGCTCACG
ACAATTGGTGAAACTCCCACACCCGAGAACGAAACGGAATATTTATTTGTTGTAGCTGAC
TTTTTGGCTGGTGTCTTGATTTTTGCTACCATCGTCGGTAATATTGGTTCAATGATTTCA
AACATGAATGTTGCCCGTGTTGAATTTCAAAACCGTATGGATGGAGTAAAACAATACATG
GCATTTCGCAAAGTCGGTGGCGAACTGGAAGCACGAGTCATTCGATGGTTTGCTTATACT
TGGGCTCAAAGTGGAGCACTCGATGAAGAGCGTGTGCTTGCTGCATTACCAGACAAGTTA
AAAGCGGAAATTGCCATTCGTGTACATATGGATACATTGAAACAAGTTAGAATATTTCAA
GATTGTGAGCCAGGTTTGCTCGAGGCATTGGTGCTCAAATTACGTTTGCAAGTCTTCAGT
CCTGGTGACTACATTTGTCGAAAAGGTGACGTGGGTAAGGAGATGTATATTGTAAAACGA
GGAAGACTTTCGGTGGTGGCTGATGATGGAACAACAGTTCTCGCAACACTCGGTGCTGGT
TCTGTTTTTGGCGAGGTTTCCGTTTTGGAAATTGCCGGTAATAGAACAGGTAATAGGAGA
ACTGCCAACGTGAGATCGATAGGATATTCAGATTTATTTTGTCTTGCAAAACGTGACCTT
TGGGAGACATTAGCAGACTACCCTGAAGCACGTGCCTCATTGACAGAGCGTGGATGTCAA
TTGCTTCGAAAGGATGGCCTTCTTGATGAAGCAGTATTTGCGAGTGCACAACAGCAACAA
GACACGCTAGAGTTAGGTGTTGCTAAATTAGAACACACAGTAGAGAATCTTAATTTACGT
TTAGCACGACTCCTTGGCGAATATACATCTTCGCAATCGAAGCTTAAGCAACGTATTTCA
AAATTGGAAGAAAAACTCTATGACACACCATTCCATAACACTGATGACAACGAAGATGAG
GAATTACGACAACGAAGATATTCACTGCAAAATGACTCGAGAACGCATCGACGTGTAAAA
AAGTTATCAACACAACCTCAACTCGATAGCGAAGATGAACTGGAACCAACGACGGAATTA
TTGTCGAGACAGAATACATTTTAG
>g4217.t1 Gene=g4217 Length=667
MVKKIEIAVISANETRCDEKLNSSNDHSYSTFRRALNALRRRISRKEHRTRPPDKFNADK
FVITNQNAMGQQQSMSGNPSDGVTSRLSFDPSLPSYYRWLAVVSIAVLYNIIFVVGRAIF
WEINKKSTLLWYTLDYLCDFIYLLDTLVHVHEGYLEQGLLVRDAKKLRQHYFSTSHWRLD
VLSMLPTDFFYFWWGPNECNSERVPCAVIVRINRLLRLPRMWEWFERTETATGYPNAFRI
CKVVLAILVLIHWNACLYFAISYAQGFGSDNWVYNLNGTQNASLTRQYIYSFYWSTLTLT
TIGETPTPENETEYLFVVADFLAGVLIFATIVGNIGSMISNMNVARVEFQNRMDGVKQYM
AFRKVGGELEARVIRWFAYTWAQSGALDEERVLAALPDKLKAEIAIRVHMDTLKQVRIFQ
DCEPGLLEALVLKLRLQVFSPGDYICRKGDVGKEMYIVKRGRLSVVADDGTTVLATLGAG
SVFGEVSVLEIAGNRTGNRRTANVRSIGYSDLFCLAKRDLWETLADYPEARASLTERGCQ
LLRKDGLLDEAVFASAQQQQDTLELGVAKLEHTVENLNLRLARLLGEYTSSQSKLKQRIS
KLEEKLYDTPFHNTDDNEDEELRQRRYSLQNDSRTHRRVKKLSTQPQLDSEDELEPTTEL
LSRQNTF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g4217.t1 | CDD | cd00038 | CAP_ED | 418 | 534 | 2.21336E-26 |
| 12 | g4217.t1 | Coils | Coil | Coil | 567 | 605 | - |
| 9 | g4217.t1 | Gene3D | G3DSA:1.10.287.70 | - | 98 | 343 | 5.2E-13 |
| 10 | g4217.t1 | Gene3D | G3DSA:1.10.287.630 | Helix hairpin bin | 344 | 409 | 4.5E-27 |
| 11 | g4217.t1 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 411 | 541 | 9.5E-40 |
| 8 | g4217.t1 | Gene3D | G3DSA:1.20.5.300 | - | 561 | 606 | 8.8E-17 |
| 27 | g4217.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 628 | 667 | - |
| 28 | g4217.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 628 | 648 | - |
| 4 | g4217.t1 | PANTHER | PTHR45638 | CYCLIC NUCLEOTIDE-GATED CATION CHANNEL SUBUNIT A | 71 | 614 | 4.2E-234 |
| 5 | g4217.t1 | PANTHER | PTHR45638:SF3 | CYCLIC NUCLEOTIDE-GATED OLFACTORY CHANNEL | 71 | 614 | 4.2E-234 |
| 2 | g4217.t1 | Pfam | PF00520 | Ion transport protein | 99 | 344 | 1.5E-22 |
| 3 | g4217.t1 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 437 | 526 | 5.1E-19 |
| 1 | g4217.t1 | Pfam | PF16526 | C-terminal leucine zipper domain of cyclic nucleotide-gated channels | 534 | 605 | 2.3E-24 |
| 15 | g4217.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 95 | - |
| 18 | g4217.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 120 | - |
| 14 | g4217.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 121 | 242 | - |
| 17 | g4217.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 243 | 264 | - |
| 16 | g4217.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 265 | 313 | - |
| 19 | g4217.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 314 | 336 | - |
| 13 | g4217.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 337 | 667 | - |
| 26 | g4217.t1 | ProSitePatterns | PS00888 | Cyclic nucleotide-binding domain signature 1. | 445 | 461 | - |
| 25 | g4217.t1 | ProSitePatterns | PS00889 | Cyclic nucleotide-binding domain signature 2. | 483 | 506 | - |
| 29 | g4217.t1 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 418 | 524 | 23.174 |
| 24 | g4217.t1 | SMART | SM00100 | cnmp_10 | 418 | 539 | 3.4E-24 |
| 6 | g4217.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 95 | 342 | 8.64E-37 |
| 7 | g4217.t1 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 346 | 542 | 5.24E-45 |
| 23 | g4217.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 99 | 121 | - |
| 22 | g4217.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 243 | 265 | - |
| 21 | g4217.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 314 | 336 | - |
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 K04950 (cyclic nucleotide gated channel alpha 3)
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