Sequence
atgc intronic sequence ATGC exonic sequenceCACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtacttcatgtcatgttgcatgtatctcacaaacattaaagctaagcaatttttttacactgttttcatcatttttctcctggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16480.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16480.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 3
CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtacttcatgtcatgttgcatgtatc-tcacaaacattaaagctaagcaatttttttacactgttttcatcatttttctcctggcag
|| |||||| |||| ||||||| || || ||||||||||||||||||||||||||||||||||| || ||||| | ||||| | || || ||||| | |||||| | | || | | | ||| || | | ||| | | | || | || | ||| |||
TACCTATGATGCATTCAAGGCCTATGTACCTGAGATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgtattc--tgtcattccgaaattagcatttttgatattctgtatatgt--tggcattataataatgatgtcttgttcccccta-cag
upper sequence: AT3G16480.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G01720.1 (Glycine max), 5'ss of exon 3
CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtactt--catgtcatgttgcatgtatctcacaaacattaaagctaagcaatttttttacactgtt-ttcatcatttttctc--ctggcag---------
||| ||||||| | || ||||||| ||| ||||||||||| | || |||| |||| |||||||| || || |||||||||||||| |||||||||||| || | ||| ||| | | ||||| || ||| | | || | ||||||||||| || || |
TACATTTGATGCATTAAAGACCTATGCTCCACAAATGGTTGAATTACTGGTTGACTGTGTAAGGAACCCAGCCTTCTTGGATTGGGAAGTCAATGAAGAGgtatttattttttcaagtttctcttttctcagggactgatcttgtaattcttaggtcagcaagctcattcatcattttcttcagctaatgggcaggcttt
upper sequence: AT3G16480.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G21380.1 (Glycine max), 5'ss of exon 3
CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtactt--catgtcatgttgcatgtatctcacaaacattaaagctaagcaatttttttacactgttttcat-catttttctcct-ggcag-------------
||| ||||||| | || ||||||||||| ||||||||||| | || |||| |||| ||| |||| || || |||||||||||||| |||||||||||| || | ||| ||| | | |||| || | || || | || || |||| ||| || || | |||
TACATTTGATGCCTTAAAGACCTATGTTCCACAAATGGTTGAATTACTGGTTGACTGTGTAAGGCACCCAGCCTTCTTGGATTGGGAAGTCAATGAAGAGgtatttattttttcaagtttctcttttctccgggact---gatcttgtcattcttaggtcagcaagctcattcatcattttcttcagcaactgggctggcttt
upper sequence: AT3G16480.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G43000.1 (Glycine max), 5'ss of exon 4
CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtactt---ca-tgtcatgt--tgcatgtatctcacaa---acattaaa---gctaagcaatttttttacactg----ttttcatcatttttctcctggcag
||| |||||||| | ||||| |||||||| ||||| |||| || | ||||| |||| |||||||| || || ||||||||||| || |||||||||||| | || | |||| | || ||| ||| | | |||||| | || | | | || ||| | | ||| |
CACTTTTGATGCTTTAAAAACTTATGTTCCACAAATGATTGAGTTGTTGATTGACTGTGTAAGGAACCCGGCCTTCTTGGATTGGGAGGTCAATGAAGAGgtatatatgcactatcatttaatgattgtctcttctgatttatattaaatgagaaggaaaacctaccaaaattgatgatttctaataaattttaaccaat--
upper sequence: AT3G16480.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 5'ss of exon 3
CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgta--cttcatgtcatgttgcatgtatctcacaaacattaaagctaagcaatttttttacactgttttcatcatttttctcctggcag--------------
||| |||||||||| || || ||||| || |||||||| ||| ||||| |||| ||||||||||||||| || |||||||||||||| |||||| ||||| || || | | || || | ||||||||| ||| || | || | | ||| || | || |||
CACTTTTGATGCTCTAAAGACTTATGTCCCTGAAATGGTCGAATTGCTTGTTGACTGTGTGAGGAACCCTGTGTTCTTGGATTGGGAAGTCAATGAACAGgtaaatctcttgaattctcaaatttaccatctttacattaaag-taaaagatgtactttta-tccttttataaggaacctgatggttattttttcttgatttMapped 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|125039738|gb|EL112007.1|EL112007EST: GAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAG CTCCGAAAGGTGAAAGTAGAGATAGGAGAATTCGCAACGAATCCAATGGGT
genomic: GAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtacttcatg ... ctcctggcagCTCCGAAAGGTGAAAGTAGAGATAGGAGAATTCGCAACGAATCCAATGGGT
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 |
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CACAATTGATGCTCTCAAAACCTATGTTCCCGAAATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCTGCTTTTTTGGATTGGGAAGTGAATGAAGAGgtacttcatgtcatgttgcatgtatctcacaaacattaaagctaagcaatttttttacactgttttcatcatttttctcctggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA