General information for g13220.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Runt-related transcription factor 1.
Parent gene
- The parent gene g13220 is located on chr_1: 28587263..28599920 (- 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 | g13220 | g13220.t1 | isoform | g13220.t1 | 28587263 | 28599920 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon1 | 28587263 | 28588005 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS1 | 28587263 | 28588005 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon2 | 28588066 | 28588281 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS2 | 28588066 | 28588281 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon3 | 28590107 | 28590205 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS3 | 28590107 | 28590205 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon4 | 28592115 | 28592228 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS4 | 28592115 | 28592228 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon5 | 28599301 | 28599409 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS5 | 28599301 | 28599409 |
| chr_1 | g13220 | g13220.t1 | exon | g13220.t1.exon6 | 28599462 | 28599920 |
| chr_1 | g13220 | g13220.t1 | cds | g13220.t1.CDS6 | 28599462 | 28599920 |
| chr_1 | g13220 | g13220.t1 | TSS | g13220.t1 | NA | NA |
| chr_1 | g13220 | g13220.t1 | TTS | g13220.t1 | NA | NA |
Sequences
>g13220.t1 Gene=g13220 Length=1740
ATGCATTTAACGGGAAATTCCGGAACTGCATCAAGCAGTGGAAATTCATCAAATAATAAT
AACAACACAAATTCAAATAGCAACAATAATAACAACAATTCTACAAGTGGATCATCAAGT
AATAATAACAATAATTCGAATAACAACAATAATAATGGCAATAGCAGCAATACCAATAAT
AACAACAATTCATCATCAAATAACAACAACAATAATCAACCGCTCACACCTGAACAAATC
CTACAAGAGACATACACGAAAATGACATCCGATATTTTGGCCGAAAGAACACTTGGTGAT
TTTCTATCAGAACATCCTGGTGAACTTATACGTACTGGTTCACCGCTATTTGTTTGTACA
GTTCTTCCGACACATTGGCGTTCAAATAAGACGCTGCCAGTCGCATTTAAAGTTGTTGCA
CTTGGTGATGTTAATGATGGAACAATGGTCACTGTTCGAGCTGGAAATGATGAAAATTAT
TGTGCAGAATTAAGAAATGCAACAGCAGTGATGAAAAATCAAATTGCAAAATTTAATGAT
CTGAGATTTGTAGGAAGAAGTGGAAGAGGCAAAAGTTTCACATTGACCATCACAATATCA
ACAAGTCCTCCACAAATAACGACCTACAATAAAGCTATAAAAGTGACTGTCGATGGACCT
CGAGAACCGAGATCAAAGACAAGGCAGCAGCAGCAATTTCATTTTGCATTTGGGCAGCGA
CCTTTTCATTTTCCAGCCGATCCACTCAGTTTTCGTATGCCACCAATTGGTAATTGTCAA
AATATGTCACAATTCAGTTTAAGCTCATCAAATACAGCACATTGGAGTTATGGGTCAACT
TCAGCATATCCACCATATTTAGCAGCTAGTGGAAGTTTGCCAGCTGCTTGTACCACACCA
ACTGCTGCACAATTTAATAATCCTGCATTAGGTTTCTCTTGCTCACCAACGGAAACGTCA
TCACAAGATTTCACTGGAGCTCGAGACTGTGTACCAATGTTACCTGATTCAACAGCAACA
GATTTAGATCAGCATTTGAGCAATTTAGTCGGAACCCCGCCATCATCAGCACAAATGAAT
CATCAAACGCTAATGAATGCAAATGTACAAGGCAATAATGAAACGCATGAAAATCTCCCA
ACAAATGGCTCAAATGGACTCGTGATAGCTCGCTATCAGAATCAAGGAAATAATGATTAC
AACTTACATACGAGTCAAAATGGTCCACGAAGTTTGAGCGATTCATCACAAGCAGAGTCA
CCAGTTCAAGATGATTTGTTAACTTCAAATACACCAAATTTGGGTTCAAATGTAAATCAA
AATTTTCAAAACCAAAATTCATATGGAAATGGCAGTAATGGCTGCAATGGTTCAATTTAT
CCCGTCTTGCCAGCAAGTCTACTCTACACACAACTTTATACTGCTGCAAATCAATCGCAT
GGCTTTCATTCGCATTCATTGCAATCACATTCATCACAGAATTCTCTAATGCATGGAGAA
TTGCAAAGTGTGATGGATCATATTGTTACTGGTACAGGTTCACATGGTGGATCACGTCAT
CAACATCATCAACAGTTGATGGCAGGAAATACAGATTTAAGCTTGATTGGAAATTGTGGA
ACAGCCGCACGCGTTGCAGATGAAAGTGTGAGTAATCGGCAATTAATTAATGGTCCTCGG
GGACAGCAATCACAGCATGCTCCTCCACCGGGCGATTCTGGTGTATGGCGTCCTTATTGA
>g13220.t1 Gene=g13220 Length=579
MHLTGNSGTASSSGNSSNNNNNTNSNSNNNNNNSTSGSSSNNNNNSNNNNNNGNSSNTNN
NNNSSSNNNNNNQPLTPEQILQETYTKMTSDILAERTLGDFLSEHPGELIRTGSPLFVCT
VLPTHWRSNKTLPVAFKVVALGDVNDGTMVTVRAGNDENYCAELRNATAVMKNQIAKFND
LRFVGRSGRGKSFTLTITISTSPPQITTYNKAIKVTVDGPREPRSKTRQQQQFHFAFGQR
PFHFPADPLSFRMPPIGNCQNMSQFSLSSSNTAHWSYGSTSAYPPYLAASGSLPAACTTP
TAAQFNNPALGFSCSPTETSSQDFTGARDCVPMLPDSTATDLDQHLSNLVGTPPSSAQMN
HQTLMNANVQGNNETHENLPTNGSNGLVIARYQNQGNNDYNLHTSQNGPRSLSDSSQAES
PVQDDLLTSNTPNLGSNVNQNFQNQNSYGNGSNGCNGSIYPVLPASLLYTQLYTAANQSH
GFHSHSLQSHSSQNSLMHGELQSVMDHIVTGTGSHGGSRHQHHQQLMAGNTDLSLIGNCG
TAARVADESVSNRQLINGPRGQQSQHAPPPGDSGVWRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g13220.t1 | Gene3D | G3DSA:2.60.40.720 | - | 95 | 234 | 3.6E-74 |
| 16 | g13220.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 15 | g13220.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 405 | 424 | - |
| 17 | g13220.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 557 | 579 | - |
| 3 | g13220.t1 | PANTHER | PTHR11950 | RUNT RELATED | 26 | 445 | 1.2E-211 |
| 5 | g13220.t1 | PANTHER | PTHR11950:SF44 | RUNT RELATED A, ISOFORM D | 26 | 445 | 1.2E-211 |
| 2 | g13220.t1 | PANTHER | PTHR11950 | RUNT RELATED | 450 | 579 | 1.2E-211 |
| 4 | g13220.t1 | PANTHER | PTHR11950:SF44 | RUNT RELATED A, ISOFORM D | 450 | 579 | 1.2E-211 |
| 6 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 96 | 115 | 1.9E-68 |
| 11 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 115 | 136 | 1.9E-68 |
| 9 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 137 | 156 | 1.9E-68 |
| 8 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 157 | 178 | 1.9E-68 |
| 7 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 179 | 200 | 1.9E-68 |
| 10 | g13220.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 201 | 223 | 1.9E-68 |
| 1 | g13220.t1 | Pfam | PF00853 | Runt domain | 100 | 226 | 1.2E-70 |
| 18 | g13220.t1 | ProSiteProfiles | PS51062 | Runt domain profile. | 97 | 225 | 68.525 |
| 12 | g13220.t1 | SUPERFAMILY | SSF49417 | p53-like transcription factors | 101 | 225 | 1.24E-63 |
| 13 | g13220.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09280 (runt-related transcription factor)
Pathway
This gene does not belong to any 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