Sequence
atgc intronic sequence ATGC exonic sequence...tataaacataggttatggaggcattttcgttgaaaaaaatgttttgcagtgattcctgatttcctgtcaagtatgtgagatgatatttttttctctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G50410.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G23390.1 (Glycine max), 3'ss of exon 6
tataaacataggttatggaggcattttcgttgaaaaaaatgttt-tgcagtgattcctgatttcctgtcaagtatgtgagat--gatatt------tttttctctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
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-----gcctag--catacacttctgcaaattctagaatatttttgttcagctgatcttgtttttctg--aagtattgtagatctgatattaaaaggttgtactttgcagGCATATGCTGCTGCTGGGACAGTGAGCCAAAACTATGCTAATATTCTTTTAATGCTTTTACGTCTCCGACAGGCTTGTGACCACCCGCTTCTTGTTAAAG
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G43430.1 (Glycine max), 3'ss of exon 8
tataaacataggttatggaggcattttcgttgaaaaaaatgttttgcagtgattcctgatttcctgtcaagt-----atgtgagatgatat-ttttttctctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
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gcctagcatacacttccgcaa-attct-----agaatatttttgttcagctgatcttatttttctgaagtgttgtagatctgatatgaaaagtttgtactttgcagGCATATGCTGCTGCTGGGACAGTGAGCCAAAACTATGCTAATATTCTTTTAATGCTTTTACGTCTCCGACAGGCTTGTGACCACCCGCTTCTTGTTAAAG
upper sequence: AT1G50410.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0071g00780.t01 (Vitis vinifera), 3'ss of exon 6
tataaacataggttatggaggcattttcgttgaaaaaaatgttttgc-agtgattcctgatttc---ctgtcaagtatgtgaga----tgatatttttttct---ctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
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-----------tttttgatgatctcttggagatcaaaactatgctgttggttataattgaagcagagttatcaagtatctggaaataatgatttttttttttgtgttgcagGAATATGCAGCTGCTGGCACTGTTAATCAAAATTATGCAAATATTCTCCTTATGCTTTTGCGACTTCGTCAGGCTTGTGACCACCCACTTCTTGTAAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125092391|gb|EL150214.1|EL150214EST: ACGTGAAGCTTGAATCCGATTCCCGTTCTCAGTTCAAG GCATATGCTGCTGCAGGAACTTTGAAT
genomic: ACGTGAAGCTTGAATCCGATTCCCGTTCTCAGTTCAAGgtgctctttc ... ttctctgcagGCATATGCTGCTGCAGGAACTTTGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagtgattcctgatttcctgtcaagtatgtgagatgatatttttttctctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
tcctgat putative branch site (score: 3)
tatttttttctctgc putative PPT
agatgatattttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataaacataggttatggaggcattttcgttgaaaaaaatgttttgcagtgattcctgatttcctgtcaagtatgtgagatgatatttttttctctgcagGCATATGCTGCTGCAGGAACTTTGAATCAAAACTATGCAAACATTCTTCTCATGCTTTTGCGACTACGCCAAGCTTGTGACCACCCCCAACTTGTTAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- -aaacata
- - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - -tgttttg