General information for g12999.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pickpocket protein 28.
Parent gene
- The parent gene g12999 is located on chr_1: 27431770..27433599 (- 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 | g12999 | g12999.t1 | isoform | g12999.t1 | 27431770 | 27433599 |
| chr_1 | g12999 | g12999.t1 | exon | g12999.t1.exon1 | 27431770 | 27431881 |
| chr_1 | g12999 | g12999.t1 | cds | g12999.t1.CDS1 | 27431770 | 27431881 |
| chr_1 | g12999 | g12999.t1 | exon | g12999.t1.exon2 | 27431935 | 27432115 |
| chr_1 | g12999 | g12999.t1 | cds | g12999.t1.CDS2 | 27431935 | 27432115 |
| chr_1 | g12999 | g12999.t1 | exon | g12999.t1.exon3 | 27432171 | 27432256 |
| chr_1 | g12999 | g12999.t1 | cds | g12999.t1.CDS3 | 27432171 | 27432256 |
| chr_1 | g12999 | g12999.t1 | exon | g12999.t1.exon4 | 27432314 | 27433599 |
| chr_1 | g12999 | g12999.t1 | cds | g12999.t1.CDS4 | 27432314 | 27433599 |
| chr_1 | g12999 | g12999.t1 | TSS | g12999.t1 | NA | NA |
| chr_1 | g12999 | g12999.t1 | TTS | g12999.t1 | NA | NA |
Sequences
>g12999.t1 Gene=g12999 Length=1665
ATGGAGATTTCCGTTTGGAAGTCTGTTACACAAGAAAGTTCCATGCATGGAGTTCATCAT
ATCACTGATGATAAAAGAAACAAACCTTCAAAGTTGTTTTGGTGCTGTGTTATACTAGCT
TCAATAACTTTGCTCTTTCTTTTTGGTTCGACCGTTTATCTAAAGTTTAACGTTGAACCT
GAAATTGGATTGCGAGTGAATCAAAAATCAATGGGAGATTTACCATTACCAGCAATCACA
ATTTGTTCACCTGTTTTTGCTCGTGATTACTTAGTTAATTATACAAAAGCTGCAGATGCA
ATTCGAGCTAAAACTTCAGTTTCCTTCACGCCTCAAGAACAAAATTATTTCGCAGCAAAC
AGTCATTCTTGTATACCAGGTTATATGAAATTTATAAATGAAAATTGCATGAATCGAACT
GATTTTAACATTATGAAACTTATGAACGAAAGTGCTCTTTATCAAAATGAAATTTTCAAA
TCATGTACATTCAGGAATATAACTTGGGATTGTGAAAAACTTTTTACTCGAATCTTTTCT
GACTATGGCTATTGTTATACTTTTAATACACTTGATCATAATCAACTCTTTAATCAAGAA
ATTATCAGTCCTGATTTTGATGTGTTTAAGAAAACTGTTCAGTTTGGAACAAACTCAACA
AGTCAATGGTCAATGTTCACCAATTACAAGAAAAATCAAACTACTTACTTTCCATCGAGA
GCTTTGAAAATCAACATTTTGGGTCTTTATACATATCTCAATGAAAACGATACAGCAAAT
AATTGTCAAGGAACAGGAAAAGTCTTTCCCATCATTCTTCACATGCCTAATGAAATACCG
ACACCATTTCATGAGGAAATGTATTTAGAATTTGGTCGTCGAAAGCAAGTTACTCTCATG
ATTAAAACTTATAAATCTACCGATGAATTAAAGAAATATTTACCAGAAAAGCGAGGTTGT
TACTTTGAAGGTGAAAGGCAATTGAAATTTTTCAAGTCCTACACAAAGGCTCATTGTGAT
TTCGAATGCATGACTAACTATACTTTGGAAGTTTGTGGTTGTGTGAAATTTTCAATGCCA
AGAACAAAAGGGACACCAATTTGTGACATTGATAAAGGCGACTGTTACTACAATGCTATG
CTGCAATGGCCGAGTAATCATGAAAACTCACATAAACCATGTAACTGTTTGGAAACGTGT
AGTTCGATCAAGTATAGCATTCTTTATGAGAGGAATTCACAGTTGAATGATTTTACTGGA
CCATCACCGGTTGCTAACACTAAAGGTGGAACTTACAGTTTTTTTTCTATTCGTTCAAGA
AATCATGTGATTGATGAATATGAAAATTTTGCTGCATATCGCTTACAAAATTTTGTTGCT
GATTTTGGTGGTCTCTTGGGATTATTTTTGGGATGTAGCATCATATCATTGGTTGAGCTT
ATTTATTTTTGTATAAATGGAATCTACAAAAAAATTAAGCACCAAGATATAAAACTTTCA
AACAAAGCGAGAGATATTAAGATTGTCAAACCAAAATTGCAGCAATTCCCAAAAAATATC
ATACCAAAAGCAGAACAGCAAAAGATTGAATTCATTCGAGCTTTGAATCCTACAAATTTG
GATTTTTATATTCAAAAGAGAATTTTGGAAGAGATAAAAAAGTGA
>g12999.t1 Gene=g12999 Length=554
MEISVWKSVTQESSMHGVHHITDDKRNKPSKLFWCCVILASITLLFLFGSTVYLKFNVEP
EIGLRVNQKSMGDLPLPAITICSPVFARDYLVNYTKAADAIRAKTSVSFTPQEQNYFAAN
SHSCIPGYMKFINENCMNRTDFNIMKLMNESALYQNEIFKSCTFRNITWDCEKLFTRIFS
DYGYCYTFNTLDHNQLFNQEIISPDFDVFKKTVQFGTNSTSQWSMFTNYKKNQTTYFPSR
ALKINILGLYTYLNENDTANNCQGTGKVFPIILHMPNEIPTPFHEEMYLEFGRRKQVTLM
IKTYKSTDELKKYLPEKRGCYFEGERQLKFFKSYTKAHCDFECMTNYTLEVCGCVKFSMP
RTKGTPICDIDKGDCYYNAMLQWPSNHENSHKPCNCLETCSSIKYSILYERNSQLNDFTG
PSPVANTKGGTYSFFSIRSRNHVIDEYENFAAYRLQNFVADFGGLLGLFLGCSIISLVEL
IYFCINGIYKKIKHQDIKLSNKARDIKIVKPKLQQFPKNIIPKAEQQKIEFIRALNPTNL
DFYIQKRILEEIKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12999.t1 | Gene3D | G3DSA:1.10.287.770 | - | 31 | 481 | 1.6E-42 |
| 11 | g12999.t1 | Gene3D | G3DSA:2.60.470.10 | - | 62 | 451 | 1.6E-42 |
| 12 | g12999.t1 | Gene3D | G3DSA:1.10.3590.10 | - | 85 | 266 | 1.6E-42 |
| 13 | g12999.t1 | Gene3D | G3DSA:1.10.287.820 | - | 312 | 400 | 1.6E-42 |
| 2 | g12999.t1 | PANTHER | PTHR11690:SF222 | ACID-SENSING ION CHANNEL 5 | 8 | 495 | 3.8E-48 |
| 3 | g12999.t1 | PANTHER | PTHR11690 | AMILORIDE-SENSITIVE SODIUM CHANNEL-RELATED | 8 | 495 | 3.8E-48 |
| 4 | g12999.t1 | PRINTS | PR01078 | Amiloride-sensitive sodium channel alpha-subunit signature | 31 | 48 | 1.7E-9 |
| 5 | g12999.t1 | PRINTS | PR01078 | Amiloride-sensitive sodium channel alpha-subunit signature | 72 | 88 | 1.7E-9 |
| 8 | g12999.t1 | PRINTS | PR01078 | Amiloride-sensitive sodium channel alpha-subunit signature | 173 | 189 | 1.7E-9 |
| 7 | g12999.t1 | PRINTS | PR01078 | Amiloride-sensitive sodium channel alpha-subunit signature | 449 | 463 | 1.7E-9 |
| 6 | g12999.t1 | PRINTS | PR01078 | Amiloride-sensitive sodium channel alpha-subunit signature | 463 | 479 | 1.7E-9 |
| 1 | g12999.t1 | Pfam | PF00858 | Amiloride-sensitive sodium channel | 11 | 483 | 1.7E-68 |
| 16 | g12999.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 31 | - |
| 18 | g12999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 54 | - |
| 17 | g12999.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 55 | 461 | - |
| 19 | g12999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 462 | 485 | - |
| 15 | g12999.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 486 | 554 | - |
| 9 | g12999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 54 | - |
| 10 | g12999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 463 | 485 | - |
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:0005272 | sodium channel activity | MF |
| GO:0006814 | sodium ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04830 (acid-sensing ion channel 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