General information for g12939.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein abrupt.
Parent gene
- The parent gene g12939 is located on chr_1: 27060495..27077178 (+ 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 | g12939 | g12939.t1 | isoform | g12939.t1 | 27060495 | 27077178 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon1 | 27060495 | 27060653 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS1 | 27060495 | 27060653 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon2 | 27060873 | 27060988 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS2 | 27060873 | 27060988 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon3 | 27061291 | 27061504 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS3 | 27061291 | 27061504 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon4 | 27061658 | 27061954 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS4 | 27061658 | 27061954 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon5 | 27062012 | 27062210 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS5 | 27062012 | 27062210 |
| chr_1 | g12939 | g12939.t1 | exon | g12939.t1.exon6 | 27076283 | 27077178 |
| chr_1 | g12939 | g12939.t1 | cds | g12939.t1.CDS6 | 27076283 | 27077178 |
| chr_1 | g12939 | g12939.t1 | TSS | g12939.t1 | NA | NA |
| chr_1 | g12939 | g12939.t1 | TTS | g12939.t1 | NA | NA |
Sequences
>g12939.t1 Gene=g12939 Length=1881
ATGGATATCTCTTCACCAACACCATCCGATCAGCAGTACGCTTTGAAATGGAATGACTTT
CAATCATCGATATTGTCATCATTTCGTCATTTACGCGATGAAGAAGACTTTGTTGATGTT
ACGTTAGCGTGCGATCAGCGATCATTTACGGCCCATAAGGTGGTATTGAGCGCATGCAGT
CCATATTTTCGTAAATTACTAAAGGCCAATCCTTGCGAACATCCAATCGTTATTCTTCGA
GACATTCGTTCCGAAGACGTGGAAAATTTGTTAAGATTTATGTACAATGGAGAAGTTCAC
ATTGGACAAGAACAGCTCAGTGATTTTCTTAAGACAGCTCATTTGCTGCAAATTCGTGGA
CTTGCCGAAGTTACCAATAGTCACCAATCACTACATAAAAGCAATCTTTCACATAATGCT
TCCATCAATCCAGCATCGATACTTCCCGCTTTGACGGCCTCGCTTAGCAAAGAGATGAGG
AATTCACCACAAAATCAAAGCTCTGTATCAATTCCATGGGATATGATTACAGATGATTCA
TCACAGCCTACGCCACCGCCACAGAAGCGAATTAAATCGGCCGAGCTTTATAAGAAACAA
CATGGACTGACTGATGACCAGTTGTTAGTGCGCGATAGTTTGCAAACAAGAGTGCAACAA
CATGCACTTCGTCGTGAACGCGATAAATCAAAAGACTCACATGATCGTGATAGAAGTTTA
GAAATGAAAGAATCACTTTTGAGTCAAGCATTGGAAGGTGGCCCAACATTGACAATTCCA
AATCAACATGCTGACTTGCAATCACTCCAGGCGCAAAGCACGGGTGAAGACAGTAATAGT
TCTGATACAGTTGCTTCCGATGCGGGTGACATGCATGACGGCTTAAATGGTTCACTTGAT
CACTCACGAACACCGACTTTTGCAAATTCTTTCCTGGGACTGCCTGGTTTATTACCTGGA
CCATCTGGCATGGGTGACAATTTCGATGCTCAACATTCACTTCTATGCGATGCTGTTATA
AAACAAGAAATCAATGATGACGACGAAGAGAATGTCAATGAAAATTTACACAATAATGAC
GATTCGAATTCTAATATAACTAATACAAATGTACATAATCCTTCGCCGAAGCGAAATTCA
AACAACACGGACGTCGTTTCTCATGAGTCTGCTGTTGGTCTCTCGACAACGATCGCTGCA
CTGCAGCAACAATCAAATCACTTTCGACAGCAACAGGAAGAGATTGTAAATAGATTGCAT
AAGGCTGTATCCGATAACTTGAAATTAATTAATCAGAGCACGGAAAGTGGTGTGAATGGG
AGTAGTACGTTTATTAGTAACAAGCAACAACAACAACAGCAAGACGATTGTGTCAATCAT
AATCTCAGTCTCAATATGAACTTAAGTGCAAACAGTCGCTTCGCAGTGCGAAACTTTAAT
GGAAATGCGTCAGAAATGAAAATGTGTCGCCTTAATAAGAGTAAATTAAGTAACTCAATT
GTTGGTGCACAGCAGCATCAACAACAATTGCATGCCAATATTGTAACGAATGATCTCTTT
TCAAGTCTTATTGATAATAATAATGATGATAATAATAATAGCAGTAGTGATTTAATTATG
AATGACGATGGAAATGTTGATGGCAATTATTTGCTTCCATGTCCATTATGTGAAATTCCT
TTAGAGCCTCGTGTCTTTCGTCAACATCTCGATCGTCATTATCCACGTGATAGTCCTATA
TGTCCTGTACTGCAATGTGGTCGACGCTTTGCTCATCCTAATAGTGTACGAAATCACATG
CGACTGAAGCATACAGTACAATGGAATAGAATGAAATCAATGCGGTCGAGTGGTGGTCCA
TTTTCATCATTGCCATATTGA
>g12939.t1 Gene=g12939 Length=626
MDISSPTPSDQQYALKWNDFQSSILSSFRHLRDEEDFVDVTLACDQRSFTAHKVVLSACS
PYFRKLLKANPCEHPIVILRDIRSEDVENLLRFMYNGEVHIGQEQLSDFLKTAHLLQIRG
LAEVTNSHQSLHKSNLSHNASINPASILPALTASLSKEMRNSPQNQSSVSIPWDMITDDS
SQPTPPPQKRIKSAELYKKQHGLTDDQLLVRDSLQTRVQQHALRRERDKSKDSHDRDRSL
EMKESLLSQALEGGPTLTIPNQHADLQSLQAQSTGEDSNSSDTVASDAGDMHDGLNGSLD
HSRTPTFANSFLGLPGLLPGPSGMGDNFDAQHSLLCDAVIKQEINDDDEENVNENLHNND
DSNSNITNTNVHNPSPKRNSNNTDVVSHESAVGLSTTIAALQQQSNHFRQQQEEIVNRLH
KAVSDNLKLINQSTESGVNGSSTFISNKQQQQQQDDCVNHNLSLNMNLSANSRFAVRNFN
GNASEMKMCRLNKSKLSNSIVGAQQHQQQLHANIVTNDLFSSLIDNNNDDNNNSSSDLIM
NDDGNVDGNYLLPCPLCEIPLEPRVFRQHLDRHYPRDSPICPVLQCGRRFAHPNSVRNHM
RLKHTVQWNRMKSMRSSGGPFSSLPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12939.t1 | CDD | cd18315 | BTB_POZ_BAB-like | 37 | 120 | 6.09208E-37 |
| 8 | g12939.t1 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 14 | 160 | 1.1E-32 |
| 7 | g12939.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 580 | 604 | 5.2E-5 |
| 14 | g12939.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 158 | 188 | - |
| 17 | g12939.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 158 | 190 | - |
| 16 | g12939.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 219 | 240 | - |
| 18 | g12939.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 356 | 388 | - |
| 15 | g12939.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 357 | 388 | - |
| 2 | g12939.t1 | PANTHER | PTHR23110 | BTB DOMAIN TRANSCRIPTION FACTOR | 9 | 144 | 7.9E-80 |
| 4 | g12939.t1 | PANTHER | PTHR23110:SF98 | PROTEIN ABRUPT | 9 | 144 | 7.9E-80 |
| 3 | g12939.t1 | PANTHER | PTHR23110 | BTB DOMAIN TRANSCRIPTION FACTOR | 265 | 334 | 7.9E-80 |
| 5 | g12939.t1 | PANTHER | PTHR23110:SF98 | PROTEIN ABRUPT | 265 | 334 | 7.9E-80 |
| 1 | g12939.t1 | Pfam | PF00651 | BTB/POZ domain | 29 | 126 | 2.8E-27 |
| 10 | g12939.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 581 | 604 | - |
| 20 | g12939.t1 | ProSiteProfiles | PS50097 | BTB domain profile. | 38 | 103 | 21.781 |
| 19 | g12939.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 579 | 609 | 9.743 |
| 11 | g12939.t1 | SMART | SM00225 | BTB_4 | 38 | 133 | 6.0E-26 |
| 13 | g12939.t1 | SMART | SM00355 | c2h2final6 | 552 | 573 | 100.0 |
| 12 | g12939.t1 | SMART | SM00355 | c2h2final6 | 579 | 604 | 0.018 |
| 6 | g12939.t1 | SUPERFAMILY | SSF54695 | POZ domain | 11 | 124 | 3.71E-30 |
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:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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