General information for g12141.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4.
Parent gene
- The parent gene g12141 is located on chr_1: 21259191..21299343 (+ 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_1 | g12141 | g12141.t2 | isoform | g12141.t2 | 21259191 | 21299343 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon1 | 21259191 | 21259588 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS1 | 21259191 | 21259588 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon2 | 21270104 | 21270275 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS2 | 21270104 | 21270275 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon3 | 21270386 | 21270624 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS3 | 21270386 | 21270624 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon4 | 21272432 | 21272595 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS4 | 21272432 | 21272595 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon5 | 21273153 | 21273289 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS5 | 21273153 | 21273289 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon6 | 21278015 | 21278152 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS6 | 21278015 | 21278152 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon7 | 21292501 | 21292650 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS7 | 21292501 | 21292650 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon8 | 21293623 | 21293699 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS8 | 21293623 | 21293699 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon9 | 21293770 | 21293911 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS9 | 21293770 | 21293911 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon10 | 21294073 | 21294242 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS10 | 21294073 | 21294242 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon11 | 21294721 | 21294815 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS11 | 21294721 | 21294815 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon12 | 21295032 | 21295120 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS12 | 21295032 | 21295120 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon13 | 21295333 | 21295520 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS13 | 21295333 | 21295520 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon14 | 21295652 | 21295771 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS14 | 21295652 | 21295771 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon15 | 21295971 | 21296077 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS15 | 21295971 | 21296077 |
| chr_1 | g12141 | g12141.t2 | exon | g12141.t2.exon16 | 21299246 | 21299343 |
| chr_1 | g12141 | g12141.t2 | cds | g12141.t2.CDS16 | 21299246 | 21299343 |
| chr_1 | g12141 | g12141.t2 | TSS | g12141.t2 | NA | NA |
| chr_1 | g12141 | g12141.t2 | TTS | g12141.t2 | NA | NA |
Sequences
>g12141.t2 Gene=g12141 Length=2484
ATGGATCTTTTAAATTGTCTTAGGGATCCGAATAATATTCCTTCAAAGGAAGTCATCTCG
TATGCAGGCAAACTAGCAAATCGAATTTTTTATAACGTTGAGGCTGATGAAGATGTTGTT
GCTGAAGCAGAAGTAGCCAGTTCTGAAGAAATGTTGCTAGAATGTAAATTGGACTTAATA
TTACAAAAAGATACTGTCAACGTTTCAAAAATTGACAACAAATTTAAATGGTTAAAGCAA
GAATTTACTTTATTCAAAAATACTGGTGAAAGAACTGAAAATCTTGAAAAACTATACAAA
GCAATTCTTTGTATCAGACCTACATCCACCGATGTTGAGCGAGTTTTTTCAGTCTCGAAT
AATTTTTGCACTAAGGTTAGGTCACGTTTGTCTGACAAATTATTTAGCGCAGCTAGTTCC
GATTCGATACGATTTCATTCAAATTTATTGAGTCATGACAATGATTTAAGAGTGTCAATT
GACAATACGTGTACAGATTCATTGGTGACAGCGTTAGATGATGAGGCACTCTTAATCAAC
GACTACATGAACGACATGTCGAAATCAAAGGTACATTTTGATGATGTGTCTCTTTATGGG
ACACCGAAAGAAGAACCGTTACCGAGCATCCCAGTAACGGCCGAAAAGACATCATCGAAT
TTTCTTAAAAATCAATTACAAGCATGGTTTCAACCGACCGACAATCGGTTGGCCATGAAA
TTATTTGGCAGCAAAAAGGCCCTTGTTAAAGAAAGAATACGACAAAAAACTGCCGGACAT
TGGGTGATTCATCCATGCAGCTCCTTTCGCTTTTATTGGGATTTGTGTATGCTGCTGTTG
CTTGTAGCTAATCTAATTATCCTACCCGTAGCCATTTCATTTTTCAATGATGATTTAAGC
ACGAGGTGGATTGCCTTCAATTGTTTAAGTGATACTATCTTTCTGGTTGACATCGTAGTA
AATTTTCGCACAGGTATCATGCAGCAGGATAATGCCGAACAAGTGATATTAGATCCAAAA
CTAATAGCCAAACATTATCTCAAAACGTGGTTTTTTCTCGATTTAATCTCATCGATTCCT
TTGGATTACATTTTTTTAATATTCAACCAGGATTTTTCCGACTCATTTCAAATTCTACAT
GCGGGGCGAGCGCTCCGCATTCTTCGTTTGGCGAAGCTACTGTCACTCGTAAGACTGCTC
CGACTTTCCAGATTGGTCCGTTATGTGTCACAATGGGAAGAAGTCTATTTCCTCAACATG
GCATCTGTGTTTATGCGAATATTCAATTTAATTTGCATGATGTTGCTCATTGGACATTGG
AGCGGTTGTTTGCAGTTTTTAGTGCCGATGCTTCAAGGATTTCCATCAAACTCATGGGTG
GCCATAAACGAGCTTCAGGAAGCATATTGGTTGGAACAATACTCTTGGGCGCTCTTTAAG
GCCATGTCACATATGTTGTGCATTGGTTACGGAAGATTTCCTCCGCAATCCCTAACTGAT
ATGTGGCTTACGATGCTATCAATGATTTCTGGAGCAACATGCTATGCACTATTTTTGGGA
CATGCGACCAATCTCATTCAGAGTTTAGACTCAAGTCGACGACAATATCGCGAAAGGGTG
AAGCAAGTGGAGGAATACATGGCGTACAGGAAACTGCCGAGAGATATGCGGCAACGCATC
ACTGAGTACTTTGAACATCGCTATCAGGGTAAATTCTTTGATGAAGAATGTATTTTGGGC
GAGCTTAGTGAGAAGTTGCGTGAGGATGTGATCAATTACAACTGTAGGTCGTTGGTTGCT
TCAGTGCCTTTTTTTGCAAATGCTGACTCAAACTTTGTATCAGATGTAGTTACCAAATTA
AGATACGAAGTTTTTCAACCTGGTGATATTATAATTAAGGAGGGAACAATAGGATCAAAA
ATGTATTTTATTCAAGAAGGAATTGTCGATATTGTTATGGCAAATGGCGAGGTTGCAACT
TCATTGTCCGATGGCTCTTATTTTGGTGAAATTTGTTTATTAACTAATGCGCGTCGTGTG
GCGAGTGTTCGAGCGGAAACTTATTGTAATTTATTTTCTTTGAGTGTCGATCATTTTAAT
GCTGTGCTTGACCAATATCCTCTTATGAGAAAAACAATGGAGACTGTAGCTGCGGAAAGA
TTAAATAAAATCGGCAAAAATCCAAATATCATGGCACAAAAAGACGAAGCCGATGACACA
AACACGATAAGTGCTGTTGTGAATGCTTTAGCCGCTGAAGCAGAAAATCATAATAATAGT
TATAGTGACGACGATGATAGTGAAAGCCCTAAGAAAATCCATTCAGAAATGAGTCTCACA
GAACTGAATCAAAGCTTAAGGATGAGCCTTCCGAGGCCAAAGAGTGAGCTCAATGTTTTC
GCGGCTACTCAGGATCCACAATTGAACCGTGATGATTTTCGCAAGTCCGATCTTCAGTTC
ACAGAGACAAGTTTTCGCTCATGA
>g12141.t2 Gene=g12141 Length=827
MDLLNCLRDPNNIPSKEVISYAGKLANRIFYNVEADEDVVAEAEVASSEEMLLECKLDLI
LQKDTVNVSKIDNKFKWLKQEFTLFKNTGERTENLEKLYKAILCIRPTSTDVERVFSVSN
NFCTKVRSRLSDKLFSAASSDSIRFHSNLLSHDNDLRVSIDNTCTDSLVTALDDEALLIN
DYMNDMSKSKVHFDDVSLYGTPKEEPLPSIPVTAEKTSSNFLKNQLQAWFQPTDNRLAMK
LFGSKKALVKERIRQKTAGHWVIHPCSSFRFYWDLCMLLLLVANLIILPVAISFFNDDLS
TRWIAFNCLSDTIFLVDIVVNFRTGIMQQDNAEQVILDPKLIAKHYLKTWFFLDLISSIP
LDYIFLIFNQDFSDSFQILHAGRALRILRLAKLLSLVRLLRLSRLVRYVSQWEEVYFLNM
ASVFMRIFNLICMMLLIGHWSGCLQFLVPMLQGFPSNSWVAINELQEAYWLEQYSWALFK
AMSHMLCIGYGRFPPQSLTDMWLTMLSMISGATCYALFLGHATNLIQSLDSSRRQYRERV
KQVEEYMAYRKLPRDMRQRITEYFEHRYQGKFFDEECILGELSEKLREDVINYNCRSLVA
SVPFFANADSNFVSDVVTKLRYEVFQPGDIIIKEGTIGSKMYFIQEGIVDIVMANGEVAT
SLSDGSYFGEICLLTNARRVASVRAETYCNLFSLSVDHFNAVLDQYPLMRKTMETVAAER
LNKIGKNPNIMAQKDEADDTNTISAVVNALAAEAENHNNSYSDDDDSESPKKIHSEMSLT
ELNQSLRMSLPRPKSELNVFAATQDPQLNRDDFRKSDLQFTETSFRS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 27 | g12141.t2 | CDD | cd00038 | CAP_ED | 604 | 713 | 1.02929E-26 |
| 13 | g12141.t2 | Gene3D | G3DSA:1.10.287.70 | - | 272 | 527 | 6.8E-8 |
| 14 | g12141.t2 | Gene3D | G3DSA:1.10.287.630 | Helix hairpin bin | 528 | 595 | 5.7E-33 |
| 15 | g12141.t2 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 596 | 724 | 1.1E-47 |
| 32 | g12141.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 797 | 827 | - |
| 4 | g12141.t2 | PANTHER | PTHR45689 | I[[H]] CHANNEL, ISOFORM E | 214 | 741 | 5.7E-281 |
| 5 | g12141.t2 | PANTHER | PTHR45689:SF4 | POTASSIUM/SODIUM HYPERPOLARIZATION-ACTIVATED CYCLIC NUCLEOTIDE-GATED CHANNEL 4 | 214 | 741 | 5.7E-281 |
| 8 | g12141.t2 | PRINTS | PR01463 | EAG/ELK/ERG potassium channel family signature | 307 | 317 | 2.6E-6 |
| 10 | g12141.t2 | PRINTS | PR01463 | EAG/ELK/ERG potassium channel family signature | 318 | 327 | 2.6E-6 |
| 7 | g12141.t2 | PRINTS | PR01463 | EAG/ELK/ERG potassium channel family signature | 436 | 446 | 2.6E-6 |
| 6 | g12141.t2 | PRINTS | PR01463 | EAG/ELK/ERG potassium channel family signature | 518 | 527 | 2.6E-6 |
| 9 | g12141.t2 | PRINTS | PR01463 | EAG/ELK/ERG potassium channel family signature | 683 | 691 | 2.6E-6 |
| 1 | g12141.t2 | Pfam | PF08412 | Ion transport protein N-terminal | 226 | 269 | 4.9E-24 |
| 2 | g12141.t2 | Pfam | PF00520 | Ion transport protein | 271 | 532 | 2.0E-20 |
| 3 | g12141.t2 | Pfam | PF00027 | Cyclic nucleotide-binding domain | 624 | 706 | 6.8E-19 |
| 21 | g12141.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 270 | - |
| 22 | g12141.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 271 | 295 | - |
| 18 | g12141.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 296 | 349 | - |
| 23 | g12141.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 350 | 368 | - |
| 20 | g12141.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 369 | 387 | - |
| 26 | g12141.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 406 | - |
| 17 | g12141.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 407 | 426 | - |
| 24 | g12141.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 448 | - |
| 19 | g12141.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 449 | 501 | - |
| 25 | g12141.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 502 | 526 | - |
| 16 | g12141.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 527 | 827 | - |
| 31 | g12141.t2 | ProSitePatterns | PS00888 | Cyclic nucleotide-binding domain signature 1. | 631 | 647 | - |
| 33 | g12141.t2 | ProSiteProfiles | PS50042 | cAMP/cGMP binding motif profile. | 604 | 720 | 26.685 |
| 30 | g12141.t2 | SMART | SM00100 | cnmp_10 | 604 | 718 | 6.2E-22 |
| 11 | g12141.t2 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 264 | 533 | 3.53E-32 |
| 12 | g12141.t2 | SUPERFAMILY | SSF51206 | cAMP-binding domain-like | 530 | 721 | 4.58E-53 |
| 28 | g12141.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 295 | - |
| 29 | g12141.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 449 | - |
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:0006813 | potassium ion transport | BP |
| GO:0005249 | voltage-gated potassium channel activity | MF |
| GO:0005216 | ion channel activity | MF |
| GO:0006811 | ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04955 (hyperpolarization activated cyclic nucleotide-gated potassium channel 2)
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