General information for g11990.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein CBFA2T2.
Parent gene
- The parent gene g11990 is located on chr_1: 20155732..20174683 (- 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 | g11990 | g11990.t1 | isoform | g11990.t1 | 20154036 | 20174683 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon1 | 20154036 | 20154344 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS1 | 20154036 | 20154344 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon2 | 20154402 | 20154566 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS2 | 20154402 | 20154566 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon3 | 20154630 | 20154968 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS3 | 20154630 | 20154968 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon4 | 20155537 | 20155732 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS4 | 20155537 | 20155732 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon5 | 20156306 | 20156601 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS5 | 20156306 | 20156601 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon6 | 20156664 | 20157004 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS6 | 20156664 | 20157004 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon7 | 20167057 | 20167150 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS7 | 20167057 | 20167150 |
| chr_1 | g11990 | g11990.t1 | exon | g11990.t1.exon8 | 20174681 | 20174683 |
| chr_1 | g11990 | g11990.t1 | cds | g11990.t1.CDS8 | 20174681 | 20174683 |
| chr_1 | g11990 | g11990.t1 | TSS | g11990.t1 | 20174997 | 20174997 |
| chr_1 | g11990 | g11990.t1 | TTS | g11990.t1 | NA | NA |
Sequences
>g11990.t1 Gene=g11990 Length=1743
ATGATGGCACTCGATGGTAAGGCAATTAAGGAGGAAATTCCGGATAAGGAAGTATACGAC
AGTGGAAGTGCTCAACAACAACAGCGGCGTGCTAAAGGCAAAGAACAGTGCCATACACCA
GATTCGCCAGAAGGTGCACGTGTCGTCGCACCACGATCGCCAATATCACCACATCACATT
CATCCTATCACAACAATGATTCCAGCAGTCACAAATCGTAGCTCGAGTGTCAATCGTCAT
AATAGTTCATCACCAACGAACGGAACACCACCGCCACCATCTGCTACAGCTTTGCTTAGT
GGAAATGCGGCACCATCTGTTCACGACAGTCAACGTTTATTGAAGATAAGAAGGTTTTTA
GGTGCTCTTGTGCAATTTGGTCAAGATACGAATCCAGATGTTGGCGATAGACTGCGTTCA
TTAGTTCTATCACTTGCTAGCAATGGATTGTCAATTGAAGAATTTCAAATAGCCGTACAG
GAGGCAACAAATTTTCCATTGCGGCCAAATGTTTTACCATTTTTGCGTTCACATTTACCA
CTGTTGCAGCGTGAAATAAACAGCATGGCTCGTGTCAGTAAACAATCTGCACTTCAATAT
GTACGGACAAATGAAAGTTCAGTAATGGAATTGTTACATAATCCAACTGATGCACATAGC
GATATATTCCTTTCGAATGACAGCAACTTTAGCAGTGGTAATGGACTAAATCTCAAAAGG
CGAGCTGCTGATGCATTACTTTACGATTCACATTTATCGAGCAGCAGTACCAATTTATCA
TCACATGAATGGAGCGACTATATTTCACCTGCAAAGCGACCACATCACTCATCATTGATG
CTCTCATCAGCCCTGCCACATTTAATAAATCATCCATCTCTGTTTGAATATCAAGCAAAT
GGCATCCATTCACATCAAGAACAACAAATGCACAATAGCCGTGAAGAACGAGACCTTCGA
TCGATAAACGCAGAAACACCATCACGTGCTAATCGAAATTCAGGAACTGGTCAAGTAAAT
GGAACAGCATCATCAGGAAGTGTCGGAAGTGGTGATGAAGAATGGCGAAACATTCATACA
ATGCTTTCGTGTATAAGTGGCATGGTTGATAAGACAAAACGAGCCATATCAATTTTACAA
CATCGTGGTAATGACACTGCATCAACAACTTCTCATCCTCATGAATCAGCCACCATCAGT
GACATTCGTCGTCAAACTGAGGAAAAAATTGCAGAATTTAGACGAAATGCTGAAGATGCT
GTCAATCAGGTTAAAAGGCAAGCAGTTTTAGAAATACAAAGGGCAGTTGCAGCAGCTGAA
ACTCGAGCACTTGAAATGATTTCACAGGAGCGCATAAAAATGGAAAAAATTTATGGTGAA
ATTAATCGAGGGCCAGATGGTATAGATGGTGAACATCAAACAACTGGATCAAATGCATGT
TGGAATTGTGGTCGCAAAGCAAATGAAACATGTTCTGGTTGCAATTTAGCACGATATTGC
GGCTCATTCTGTCAGCATAAAGACTGGGAAAGTCACCATCAGGCTTGTGGTACAAATGCA
GCACGCTCCGCAGAATCATCGCAGTCTCAAGTCACAGCGGTTGTTACAACAGCACAAAAA
ACCACACCGACTCAACAAACTTTAACACGTTCATCTGCAAATGCCAGTTCAAACAGTTCT
TCGCGTTCGTCACCACCAAATCAAACCTCATCATCTAATGGTATAACTTCACCGCCGAAA
TGA
>g11990.t1 Gene=g11990 Length=580
MMALDGKAIKEEIPDKEVYDSGSAQQQQRRAKGKEQCHTPDSPEGARVVAPRSPISPHHI
HPITTMIPAVTNRSSSVNRHNSSSPTNGTPPPPSATALLSGNAAPSVHDSQRLLKIRRFL
GALVQFGQDTNPDVGDRLRSLVLSLASNGLSIEEFQIAVQEATNFPLRPNVLPFLRSHLP
LLQREINSMARVSKQSALQYVRTNESSVMELLHNPTDAHSDIFLSNDSNFSSGNGLNLKR
RAADALLYDSHLSSSSTNLSSHEWSDYISPAKRPHHSSLMLSSALPHLINHPSLFEYQAN
GIHSHQEQQMHNSREERDLRSINAETPSRANRNSGTGQVNGTASSGSVGSGDEEWRNIHT
MLSCISGMVDKTKRAISILQHRGNDTASTTSHPHESATISDIRRQTEEKIAEFRRNAEDA
VNQVKRQAVLEIQRAVAAAETRALEMISQERIKMEKIYGEINRGPDGIDGEHQTTGSNAC
WNCGRKANETCSGCNLARYCGSFCQHKDWESHHQACGTNAARSAESSQSQVTAVVTTAQK
TTPTQQTLTRSSANASSNSSSRSSPPNQTSSSNGITSPPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11990.t1 | Coils | Coil | Coil | 403 | 423 | - |
| 13 | g11990.t1 | Gene3D | G3DSA:1.20.120.1110 | - | 109 | 214 | 6.9E-35 |
| 12 | g11990.t1 | Gene3D | G3DSA:3.30.60.180 | - | 466 | 523 | 3.1E-21 |
| 17 | g11990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 93 | - |
| 20 | g11990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 67 | 85 | - |
| 18 | g11990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 325 | 352 | - |
| 21 | g11990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 325 | 351 | - |
| 19 | g11990.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 538 | 580 | - |
| 4 | g11990.t1 | PANTHER | PTHR10379 | MTG8 ETO EIGHT TWENTY ONE PROTEIN | 35 | 556 | 6.5E-144 |
| 5 | g11990.t1 | PANTHER | PTHR10379:SF14 | NERVY, ISOFORM D | 35 | 556 | 6.5E-144 |
| 9 | g11990.t1 | PRINTS | PR01875 | Eight-Twenty-One (ETO) family signature | 149 | 177 | 3.3E-43 |
| 7 | g11990.t1 | PRINTS | PR01875 | Eight-Twenty-One (ETO) family signature | 183 | 203 | 3.3E-43 |
| 8 | g11990.t1 | PRINTS | PR01875 | Eight-Twenty-One (ETO) family signature | 423 | 451 | 3.3E-43 |
| 6 | g11990.t1 | PRINTS | PR01875 | Eight-Twenty-One (ETO) family signature | 491 | 519 | 3.3E-43 |
| 2 | g11990.t1 | Pfam | PF07531 | NHR1 homology to TAF | 114 | 200 | 3.4E-26 |
| 3 | g11990.t1 | Pfam | PF08788 | NHR2 domain like | 353 | 380 | 4.9E-8 |
| 1 | g11990.t1 | Pfam | PF01753 | MYND finger | 480 | 516 | 2.6E-7 |
| 16 | g11990.t1 | ProSitePatterns | PS01360 | Zinc finger MYND-type signature. | 480 | 516 | - |
| 23 | g11990.t1 | ProSiteProfiles | PS51119 | TAFH/NHR1 domain profile. | 110 | 205 | 27.942 |
| 22 | g11990.t1 | ProSiteProfiles | PS50865 | Zinc finger MYND-type profile. | 480 | 516 | 12.285 |
| 15 | g11990.t1 | SMART | SM00549 | nervy_1 | 112 | 202 | 1.2E-30 |
| 10 | g11990.t1 | SUPERFAMILY | SSF158553 | TAFH domain-like | 114 | 212 | 1.19E-28 |
| 11 | g11990.t1 | SUPERFAMILY | SSF144232 | HIT/MYND zinc finger-like | 476 | 518 | 3.14E-10 |
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:0045892 | negative regulation of transcription, DNA-templated | BP |
| GO:0003714 | transcription corepressor activity | MF |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K10053 (CBFA2/RNUX1 translocation partner 1)
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.
