Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgatctactattactatctcccaagtataaggatgatgtgttacttctataactgttttctcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13580.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 2
---------gtaatatgatctactattactatctcccaagtataaggatgatgtgttacttctataactgttttctcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
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gtaaggaaccacttaagttgtattgttataatgtcactgac-tatagatgatgatctggttgtatgttgatg--ctaatgttacaa---atctgtt---gactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG
upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 3
gtaatatgatctactattactatctcccaagtataaggatgatgtgttacttctataactgtt----ttctcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
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gtaattaattaatttattaatgtatcataa-cattatgctagtatattgtctttttggttattgttgtttttattgctaaatggaatt-tatgtaatgtcagTATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
-----------------gtaata-tgatctactattactatctcccaag-tataaggatgatgtgttacttctataactgttttc--tcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
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gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGMapped 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|124962655|gb|EL037043.1|EL037043EST: CTGCTTTTCATTATCCGTATCCGTGG TATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTT
genomic: CTGCTTTTCATTATCCGTATCCGTGGgtaatatgat ... ctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttacttctataactgttttctcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
ctataac putative branch site (score: 3)
ttttctcatttttcta putative PPT
atttttctatctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgatctactattactatctcccaagtataaggatgatgtgttacttctataactgttttctcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG