General information for g13219.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Segmentation protein Runt.
Parent gene
- The parent gene g13219 is located on chr_1: 28554095..28570929 (+ 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 | g13219 | g13219.t1 | isoform | g13219.t1 | 28554095 | 28570929 |
| chr_1 | g13219 | g13219.t1 | exon | g13219.t1.exon1 | 28554095 | 28554596 |
| chr_1 | g13219 | g13219.t1 | cds | g13219.t1.CDS1 | 28554095 | 28554596 |
| chr_1 | g13219 | g13219.t1 | exon | g13219.t1.exon2 | 28563054 | 28563147 |
| chr_1 | g13219 | g13219.t1 | cds | g13219.t1.CDS2 | 28563054 | 28563147 |
| chr_1 | g13219 | g13219.t1 | exon | g13219.t1.exon3 | 28563460 | 28563551 |
| chr_1 | g13219 | g13219.t1 | cds | g13219.t1.CDS3 | 28563460 | 28563551 |
| chr_1 | g13219 | g13219.t1 | exon | g13219.t1.exon4 | 28569890 | 28570078 |
| chr_1 | g13219 | g13219.t1 | cds | g13219.t1.CDS4 | 28569890 | 28570078 |
| chr_1 | g13219 | g13219.t1 | exon | g13219.t1.exon5 | 28570133 | 28570929 |
| chr_1 | g13219 | g13219.t1 | cds | g13219.t1.CDS5 | 28570133 | 28570929 |
| chr_1 | g13219 | g13219.t1 | TSS | g13219.t1 | NA | NA |
| chr_1 | g13219 | g13219.t1 | TTS | g13219.t1 | NA | NA |
Sequences
>g13219.t1 Gene=g13219 Length=1674
ATGCATATTGCATCTGAAGTGACTTCAACGACGGCTCCACCGTCGGAACAAAGTGTTAAA
AATAATGTTGAAAGTGCAAATTCAAATACAACAACGACGACAAATTCTGGTGCTAATAAT
CAAAGAAATTCTTCATCAACACCTCAACAGCAGAATACAACAACAAATGGAGGAAGTATT
GGTCGTGATTCACCATTAACAGCTGAAAATTTGGCAGAAAGAACAATTGATTCACTTATT
GCAGAGCATCCAGGTGAACTCACACGAACGGGGTCACCTCATATTGTTTGTACAGTTCTT
CCAACGCACTGGCGTTCAAATAAAACACTGCCAGTTGCCTTCAAAGTTGTAGCACTTGGT
GATGTACAAGATGGAACTGTAGTTCATTTAATGTGTGGAAATGATGAAAATTTTCATGGT
GAATTAAGAAATTGTACAACAGTAATGAAAAATCAAGTCGCAAAATTTAATGATTTAAGA
TTTGTTGGAAGAAGTGGAAGAGGAAAAAGTTTTACGCTTACTATTATTATATCGACAACA
CCAGTTCAAGTTGCGACTTATACAAAGGCAATTAAAGTGACTGTCGATGGTCCACGAGAG
CCACGCAGTAAAGTACGACACCAGGGCTTCCATCCATTTGCATTTGGTCCACGTTTTACT
GCTGATCCGCTGATTCCTTTCAAATTAGGTTTCCCTCATCATTTGACGGGTATACCCTCA
TCACAAGGAGCTCATTTGGCAGGGTCAACAGATTGGCGAATGCTCAATAATCGACCTTTT
CCACCATCACAATACTTTCATCATCATCCGCATTTTGCAGCACATAATATGTTGACGGCA
GCAATTGATCGAATGGATCGAAATTTCATCGATGGAAATAATTCAATCACTGGTCAAACA
AAAGCGAGTAGTAGCAGTCCAGATGATGAAGGAATTACAAAAGTTACAGAAATTTCATCA
TCAAAAGAGGATGACCTTGATAATGATAATGAAAATATTTCAGTAACTGGTAGTTGCTCG
CCTGACATTTCTTGCGTGAGTGAATCAGAAAATAATGGCGATGCCAAAATTGAATCGGGT
GCATTCACATCAATTGTTCAGAAGAATCGTAAATCCGAATTTATGTCACAATTTCCTGTC
AATTCACACTTTACTGGCACTACAAATCCAATGATAAATCACGCATTGGCCGCACATTTG
TTCTTTCAGAATCCACTGCTGCCGCCACCAAATCAATGGCTCTACAACCAATTGTACAAT
AATTATCATGATTTTCCGTGGTTGAGACATACACTCGCGGCCAATTCATTAACATCAACT
GAAAATTCAACAACAAATGCACGAAATGATGCGTCATCATCATCAACAACGTCTGGATTG
AGTTTTATCAAACGATCAATTACTTTGTTAACAAATAATAGCAGCATGAGTGAGAAAGAA
AACGATTCTGATGTGCAATCATCTTCATCACCTCCAGTTACATCTACAAAACGTTCACCA
AGTCCTGAAATGCCTCTAGAGTCAATTAGCTGCAAAAGAAAACGCTCATCAAGCAGCGAT
TCAATAAGTAAAGAAAATGTTGTGACAGAAATGACAAGAAAAACTGAAAATTTCATTAAC
CGAAGTCGCATTGGAGCGGGAGTGAAACAAAATGATGTATGGCGACCTTATTAG
>g13219.t1 Gene=g13219 Length=557
MHIASEVTSTTAPPSEQSVKNNVESANSNTTTTTNSGANNQRNSSSTPQQQNTTTNGGSI
GRDSPLTAENLAERTIDSLIAEHPGELTRTGSPHIVCTVLPTHWRSNKTLPVAFKVVALG
DVQDGTVVHLMCGNDENFHGELRNCTTVMKNQVAKFNDLRFVGRSGRGKSFTLTIIISTT
PVQVATYTKAIKVTVDGPREPRSKVRHQGFHPFAFGPRFTADPLIPFKLGFPHHLTGIPS
SQGAHLAGSTDWRMLNNRPFPPSQYFHHHPHFAAHNMLTAAIDRMDRNFIDGNNSITGQT
KASSSSPDDEGITKVTEISSSKEDDLDNDNENISVTGSCSPDISCVSESENNGDAKIESG
AFTSIVQKNRKSEFMSQFPVNSHFTGTTNPMINHALAAHLFFQNPLLPPPNQWLYNQLYN
NYHDFPWLRHTLAANSLTSTENSTTNARNDASSSSTTSGLSFIKRSITLLTNNSSMSEKE
NDSDVQSSSSPPVTSTKRSPSPEMPLESISCKRKRSSSSDSISKENVVTEMTRKTENFIN
RSRIGAGVKQNDVWRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g13219.t1 | Gene3D | G3DSA:2.60.40.720 | - | 73 | 210 | 8.5E-70 |
| 12 | g13219.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 65 | - |
| 13 | g13219.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 63 | - |
| 11 | g13219.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 473 | 503 | - |
| 15 | g13219.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 473 | 535 | - |
| 14 | g13219.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 521 | 535 | - |
| 2 | g13219.t1 | PANTHER | PTHR11950:SF45 | RUNT RELATED B | 21 | 557 | 5.2E-132 |
| 3 | g13219.t1 | PANTHER | PTHR11950 | RUNT RELATED | 21 | 557 | 5.2E-132 |
| 9 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 74 | 93 | 1.3E-62 |
| 5 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 93 | 114 | 1.3E-62 |
| 8 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 115 | 134 | 1.3E-62 |
| 4 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 135 | 156 | 1.3E-62 |
| 7 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 157 | 178 | 1.3E-62 |
| 6 | g13219.t1 | PRINTS | PR00967 | Acute myeloid leukemia 1 protein signature | 179 | 201 | 1.3E-62 |
| 1 | g13219.t1 | Pfam | PF00853 | Runt domain | 78 | 204 | 1.6E-66 |
| 17 | g13219.t1 | ProSiteProfiles | PS51062 | Runt domain profile. | 75 | 203 | 64.596 |
| 10 | g13219.t1 | SUPERFAMILY | SSF49417 | p53-like transcription factors | 80 | 203 | 1.99E-61 |
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