Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein abrupt.

Parent gene

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.t2 isoform g12939.t2 27060495 27077178
chr_1 g12939 g12939.t2 exon g12939.t2.exon1 27060495 27060653
chr_1 g12939 g12939.t2 cds g12939.t2.CDS1 27060495 27060653
chr_1 g12939 g12939.t2 exon g12939.t2.exon2 27060873 27060988
chr_1 g12939 g12939.t2 cds g12939.t2.CDS2 27060873 27060988
chr_1 g12939 g12939.t2 exon g12939.t2.exon3 27061291 27061517
chr_1 g12939 g12939.t2 cds g12939.t2.CDS3 27061291 27061517
chr_1 g12939 g12939.t2 exon g12939.t2.exon4 27061701 27061954
chr_1 g12939 g12939.t2 cds g12939.t2.CDS4 27061701 27061954
chr_1 g12939 g12939.t2 exon g12939.t2.exon5 27062012 27062210
chr_1 g12939 g12939.t2 cds g12939.t2.CDS5 27062012 27062210
chr_1 g12939 g12939.t2 exon g12939.t2.exon6 27076283 27077178
chr_1 g12939 g12939.t2 cds g12939.t2.CDS6 27076283 27077178
chr_1 g12939 g12939.t2 TSS g12939.t2 NA NA
chr_1 g12939 g12939.t2 TTS g12939.t2 NA NA

Sequences

>g12939.t2 Gene=g12939 Length=1851
ATGGATATCTCTTCACCAACACCATCCGATCAGCAGTACGCTTTGAAATGGAATGACTTT
CAATCATCGATATTGTCATCATTTCGTCATTTACGCGATGAAGAAGACTTTGTTGATGTT
ACGTTAGCGTGCGATCAGCGATCATTTACGGCCCATAAGGTGGTATTGAGCGCATGCAGT
CCATATTTTCGTAAATTACTAAAGGCCAATCCTTGCGAACATCCAATCGTTATTCTTCGA
GACATTCGTTCCGAAGACGTGGAAAATTTGTTAAGATTTATGTACAATGGAGAAGTTCAC
ATTGGACAAGAACAGCTCAGTGATTTTCTTAAGACAGCTCATTTGCTGCAAATTCGTGGA
CTTGCCGAAGTTACCAATAGTCACCAATCACTACATAAAAGCAATCTTTCACATAATGCT
TCCATCAATCCAGCATCGATACTTCCCGCTTTGACGGCCTCGCTTAGCAAAGAGATGAGG
AATTCACCAGTTAGTCGAATAGATGATTCATCACAGCCTACGCCACCGCCACAGAAGCGA
ATTAAATCGGCCGAGCTTTATAAGAAACAACATGGACTGACTGATGACCAGTTGTTAGTG
CGCGATAGTTTGCAAACAAGAGTGCAACAACATGCACTTCGTCGTGAACGCGATAAATCA
AAAGACTCACATGATCGTGATAGAAGTTTAGAAATGAAAGAATCACTTTTGAGTCAAGCA
TTGGAAGGTGGCCCAACATTGACAATTCCAAATCAACATGCTGACTTGCAATCACTCCAG
GCGCAAAGCACGGGTGAAGACAGTAATAGTTCTGATACAGTTGCTTCCGATGCGGGTGAC
ATGCATGACGGCTTAAATGGTTCACTTGATCACTCACGAACACCGACTTTTGCAAATTCT
TTCCTGGGACTGCCTGGTTTATTACCTGGACCATCTGGCATGGGTGACAATTTCGATGCT
CAACATTCACTTCTATGCGATGCTGTTATAAAACAAGAAATCAATGATGACGACGAAGAG
AATGTCAATGAAAATTTACACAATAATGACGATTCGAATTCTAATATAACTAATACAAAT
GTACATAATCCTTCGCCGAAGCGAAATTCAAACAACACGGACGTCGTTTCTCATGAGTCT
GCTGTTGGTCTCTCGACAACGATCGCTGCACTGCAGCAACAATCAAATCACTTTCGACAG
CAACAGGAAGAGATTGTAAATAGATTGCATAAGGCTGTATCCGATAACTTGAAATTAATT
AATCAGAGCACGGAAAGTGGTGTGAATGGGAGTAGTACGTTTATTAGTAACAAGCAACAA
CAACAACAGCAAGACGATTGTGTCAATCATAATCTCAGTCTCAATATGAACTTAAGTGCA
AACAGTCGCTTCGCAGTGCGAAACTTTAATGGAAATGCGTCAGAAATGAAAATGTGTCGC
CTTAATAAGAGTAAATTAAGTAACTCAATTGTTGGTGCACAGCAGCATCAACAACAATTG
CATGCCAATATTGTAACGAATGATCTCTTTTCAAGTCTTATTGATAATAATAATGATGAT
AATAATAATAGCAGTAGTGATTTAATTATGAATGACGATGGAAATGTTGATGGCAATTAT
TTGCTTCCATGTCCATTATGTGAAATTCCTTTAGAGCCTCGTGTCTTTCGTCAACATCTC
GATCGTCATTATCCACGTGATAGTCCTATATGTCCTGTACTGCAATGTGGTCGACGCTTT
GCTCATCCTAATAGTGTACGAAATCACATGCGACTGAAGCATACAGTACAATGGAATAGA
ATGAAATCAATGCGGTCGAGTGGTGGTCCATTTTCATCATTGCCATATTGA

>g12939.t2 Gene=g12939 Length=616
MDISSPTPSDQQYALKWNDFQSSILSSFRHLRDEEDFVDVTLACDQRSFTAHKVVLSACS
PYFRKLLKANPCEHPIVILRDIRSEDVENLLRFMYNGEVHIGQEQLSDFLKTAHLLQIRG
LAEVTNSHQSLHKSNLSHNASINPASILPALTASLSKEMRNSPVSRIDDSSQPTPPPQKR
IKSAELYKKQHGLTDDQLLVRDSLQTRVQQHALRRERDKSKDSHDRDRSLEMKESLLSQA
LEGGPTLTIPNQHADLQSLQAQSTGEDSNSSDTVASDAGDMHDGLNGSLDHSRTPTFANS
FLGLPGLLPGPSGMGDNFDAQHSLLCDAVIKQEINDDDEENVNENLHNNDDSNSNITNTN
VHNPSPKRNSNNTDVVSHESAVGLSTTIAALQQQSNHFRQQQEEIVNRLHKAVSDNLKLI
NQSTESGVNGSSTFISNKQQQQQQDDCVNHNLSLNMNLSANSRFAVRNFNGNASEMKMCR
LNKSKLSNSIVGAQQHQQQLHANIVTNDLFSSLIDNNNDDNNNSSSDLIMNDDGNVDGNY
LLPCPLCEIPLEPRVFRQHLDRHYPRDSPICPVLQCGRRFAHPNSVRNHMRLKHTVQWNR
MKSMRSSGGPFSSLPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g12939.t2 CDD cd18315 BTB_POZ_BAB-like 37 120 5.70557E-37
6 g12939.t2 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 14 158 1.1E-32
5 g12939.t2 Gene3D G3DSA:3.30.160.60 Classic Zinc Finger 570 594 5.1E-5
13 g12939.t2 MobiDBLite mobidb-lite consensus disorder prediction 158 178 -
16 g12939.t2 MobiDBLite mobidb-lite consensus disorder prediction 158 180 -
12 g12939.t2 MobiDBLite mobidb-lite consensus disorder prediction 209 230 -
15 g12939.t2 MobiDBLite mobidb-lite consensus disorder prediction 346 378 -
14 g12939.t2 MobiDBLite mobidb-lite consensus disorder prediction 347 378 -
2 g12939.t2 PANTHER PTHR23110 BTB DOMAIN TRANSCRIPTION FACTOR 9 324 2.6E-80
3 g12939.t2 PANTHER PTHR23110:SF98 PROTEIN ABRUPT 9 324 2.6E-80
1 g12939.t2 Pfam PF00651 BTB/POZ domain 29 126 2.7E-27
8 g12939.t2 ProSitePatterns PS00028 Zinc finger C2H2 type domain signature. 571 594 -
18 g12939.t2 ProSiteProfiles PS50097 BTB domain profile. 38 103 21.781
17 g12939.t2 ProSiteProfiles PS50157 Zinc finger C2H2 type domain profile. 569 599 9.743
9 g12939.t2 SMART SM00225 BTB_4 38 133 6.0E-26
11 g12939.t2 SMART SM00355 c2h2final6 542 563 100.0
10 g12939.t2 SMART SM00355 c2h2final6 569 594 0.018
4 g12939.t2 SUPERFAMILY SSF54695 POZ domain 11 124 3.61E-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