General information for g12940.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein abrupt.
Parent gene
- The parent gene g12940 is located on chr_1: 27078643..27079809 (+ 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 | g12940 | g12940.t1 | isoform | g12940.t1 | 27078643 | 27079809 |
| chr_1 | g12940 | g12940.t1 | exon | g12940.t1.exon1 | 27078643 | 27079084 |
| chr_1 | g12940 | g12940.t1 | cds | g12940.t1.CDS1 | 27078643 | 27079084 |
| chr_1 | g12940 | g12940.t1 | exon | g12940.t1.exon2 | 27079144 | 27079293 |
| chr_1 | g12940 | g12940.t1 | cds | g12940.t1.CDS2 | 27079144 | 27079293 |
| chr_1 | g12940 | g12940.t1 | exon | g12940.t1.exon3 | 27079361 | 27079809 |
| chr_1 | g12940 | g12940.t1 | cds | g12940.t1.CDS3 | 27079361 | 27079809 |
| chr_1 | g12940 | g12940.t1 | TTS | g12940.t1 | 27079966 | 27079966 |
| chr_1 | g12940 | g12940.t1 | TSS | g12940.t1 | NA | NA |
Sequences
>g12940.t1 Gene=g12940 Length=1041
ATGCGTGTTCGTGCCACTGATCCAAGACCATGTCCAAAATGCGGAAAAATCTATCGTTCA
GCACATACATTGAGAACTCACTTGGAAGATAAGCATACAATTTGTCCAGGCTATCGATGC
GTTCTTTGTGGAACTGTTGCCAAATCACGCAATTCCTTGCATTCGCACATGTCTCGTCAG
CATCGTGGAATTTCAACAAAAGATCTCCCAGTGCTGCCGATGCCAAGCCCGTTTGATCCC
GAACTTGCATCAAAATTATTAGCAAAAGCAGGTGTCAATATTTCAGCAGCAGAACTTCGC
GCAAGAGCATCACCAACTGGTACACGACGATCGGATATGAAAATGGAAATGAGAAGCAAT
GATGATAGTGATCTTGATGATCCTGAAGACTTGACAATGGCACAAGGAAGCAATAAATTT
AATTCTGGATTTTCACCAAACCCATTTAATCATCCGAGCACAACAATAACACGTGTTAGA
CAAGATGCACAAAAATTAATGGAAGCAGCACATAAAGAAAATCCTTTACAACATGGTTCT
GGTTCGGCACTTCTTGATACTTATTTGCAGTTTATCACAGAAAATTCATTTGGTTCAATG
GGAATGTCACAAGAGCAAGCAGCCGCAGCAATACAAGCAGCAAAATTCGCACAAAAAATG
GCATTAGAAAGAAATCTTGATAAGCTTCCGCCCAATTTCTTCCCACCACAACTCGATATA
TCGAAAATTCCGGGTCTGAGCGCAGCAGCAAATGATGCAACAAAAAATCTCAATTTACCA
AACGTCACAATCGAGCCTGCGAATCATTCCAACTCTGGCCACAAGTCACATAACATGTCA
AGTGGCAGTGGCTTGGACATTCGTCGCAGTGAAAGCTCCGATCGTCATGATCGTCATTCG
CCCGAACAAAATTCATTGAACATAAATAATAATAATAGTAGCAATACAAATAACAATAAT
TTAAATAATTTTAATAAAGAAGAAAGTTCAGCTGATGAGCGCAATATGTCGGATGATGAG
AGTAGCATTGCTGTTAATTGA
>g12940.t1 Gene=g12940 Length=346
MRVRATDPRPCPKCGKIYRSAHTLRTHLEDKHTICPGYRCVLCGTVAKSRNSLHSHMSRQ
HRGISTKDLPVLPMPSPFDPELASKLLAKAGVNISAAELRARASPTGTRRSDMKMEMRSN
DDSDLDDPEDLTMAQGSNKFNSGFSPNPFNHPSTTITRVRQDAQKLMEAAHKENPLQHGS
GSALLDTYLQFITENSFGSMGMSQEQAAAAIQAAKFAQKMALERNLDKLPPNFFPPQLDI
SKIPGLSAAANDATKNLNLPNVTIEPANHSNSGHKSHNMSSGSGLDIRRSESSDRHDRHS
PEQNSLNINNNNSSNTNNNNLNNFNKEESSADERNMSDDESSIAVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12940.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 7 | 71 | 1.1E-8 |
| 13 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 101 | 127 | - |
| 9 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 105 | 121 | - |
| 11 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 266 | 287 | - |
| 12 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 266 | 346 | - |
| 10 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 288 | 302 | - |
| 14 | g12940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 303 | 326 | - |
| 2 | g12940.t1 | PANTHER | PTHR23110 | BTB DOMAIN TRANSCRIPTION FACTOR | 1 | 341 | 6.5E-82 |
| 3 | g12940.t1 | PANTHER | PTHR23110:SF98 | PROTEIN ABRUPT | 1 | 341 | 6.5E-82 |
| 1 | g12940.t1 | Pfam | PF00096 | Zinc finger, C2H2 type | 10 | 32 | 0.014 |
| 6 | g12940.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 11 | 32 | - |
| 16 | g12940.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 9 | 33 | 9.141 |
| 15 | g12940.t1 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 38 | 66 | 8.891 |
| 8 | g12940.t1 | SMART | SM00355 | c2h2final6 | 9 | 32 | 0.058 |
| 7 | g12940.t1 | SMART | SM00355 | c2h2final6 | 38 | 61 | 0.023 |
| 4 | g12940.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 8 | 57 | 2.68E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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