Sequence
atgc intronic sequence ATGC exonic sequenceGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaaagcgaacaccctaactaacaatgttcttcttcatttcgatatatgagtcttaagctaaaactgtatacttgcgttgttggcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23990.1 |
intron # | 15 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 17
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaata--aaaagcgaacaccctaactaacaatgttcttcttca---tttcgat---atatgagtcttaagctaaa------actgtatac-ttgcgttgttggcag-------------------------------------------------------------------------------
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GTGAATATGTGGACATGGTGAAGGCTGGTATCATTGACCCACTAAAAGTGATCAGAACTGCCTTGGTGGATGCTGCAAGgtaagctctcaagttcatggttctgtgctttagttctttacattaaattgttgatcaaacatgggtgatacactgaagcacccacctcatcccttgtgcttatttcggtttttgatctgaaatttttcacccatttaacgttacttttggctcttgcgggttcttacaagttgtttgccttctgcag
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 17
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaa-ataaaaagcgaac-accctaactaacaatgt-tcttcttcattt--cgatatatgagt--ctta-agctaaa-actgtat-acttgcgttgttggcag----------------------------------------------------------------
|||||||||| |||||||| ||||||||||||||||||||| |||| ||||| |||||||| ||||||||||| || ||||| || || | | || || ||| | || | |||| | ||| | | | |||| ||| ||| ||| | | | | | |
GTGAATATGTTGATATGGTTAAAGCTGGAATCATAGACCCTTTGAAGGTGATTAGGACAGCCTTGGTTGATGCAGCCAGgtaggatgttcagaaatttgctgtagatattgatgcattttaattatttgttgttatgtaacttgcttatagccaaatgatgtgtgatctatatagcctacctctccttatgagataaaacctttttttgtttattatgcaacttgcttatgaccctttttgtgcag
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 17
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaa-----taaaaagcgaacaccctaactaacaatgttct--tcttcatttcgatatatgagt----cttaagctaaaactgt-atacttgcgttgttggcag------------------------------------------------------------------
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GTGAATATGTTGATATGGTTAAAGCTGGAATCATAGACCCCTTGAAGGTGATTAGGACAGCCTTGGTTGATGCAGCCAGgtaggatgtccagaaatttgttgtagatattgaaaacattttaattatttgtttgttatgtaacttgcttttaaccgaataatgtcatgtgttctatatagccaacctctccttgtgagataagaccccattttggttattatgtaactttcttatgaccttcctgtgcag
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 17
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaaagcgaacaccctaactaacaatgttcttcttcatttcgatatatgagtcttaagctaaaactgtatacttgcgttgttggcag
|||||||||| |||||||| |||||||||||||| || || |||| || || ||||| || ||||||||||| || ||||| | ||| | | | || | | || ||| | | |||| ||| || | ||| || ||| |
GTGAATATGTTGATATGGTTAAAGCTGGAATCATTGATCCATTGAAGGTTATTAGGACCGCCTTGGTTGATGCAGCCAGgtaggatgttgggaaacttgccgttagatattgatgtatttggttt-gttttatgtagctttgcttatca--atatttttctcttgcag----
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 17
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaaagcgaacaccctaactaacaa-tgttcttcttcatttcgatatatgagtcttaagctaaaactgtatacttgc-gttgttg--gcag
|||||||||| |||||||| ||||||||||| || || || |||||||| || || |||||||||||||||||||| |||||| || | | | || | | || |||| || || | | || | | ||| | ||| |||| | ||| ||||
GTGAATATGTTGATATGGTCAAAGCTGGAATTATTGATCCACTGAAAGTAATTAGAACAGCTTTGGTTGATGCTGCAAGgtaagccaaggacc--ccctttagtttttgcctcttacaattcagttatatcattcattccttaaataagaagccatatttgctgcctttgatgcag
upper sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 5'ss of exon 16
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaaagcgaacaccctaactaacaatgttcttcttcatttcgatatatgagtcttaagctaaaactgtatacttgcgttgt-tggcag-----------------------------------------
| || || ||||||||||||||||||||||| || |||||| ||||||| ||||| || || || || ||||| || |||||| ||| | ||| | || | | | | || | | | | ||| | | | | | ||| | | ||
GAGAGTACGTGGATATGGTGAAAGCTGGAATTATTGACCCTGTGAAAGTAATCAGAACCGCATTCGTCGATGCAGCAAGgtaatggaaattcttgtctccttgatt-cagggctatcaatagattggtcagacactccctaatcagcgagatttttcaaacgtcctctaacattatttggtaatccctaacgtctcttcattttgagggtgtagMapped 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|47827837|gb|CK117521.1|CK117521EST: ATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG TGTGTCATCTTTGTTGACGACAACGGAAGCTGTAGTGGTTGATCTTCCGAA
genomic: ATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaa ... ttgttggcagTGTGTCATCTTTGTTGACGACAACGGAAGCTGTAGTGGTTGATCTTCCGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAGgtaaataaaaagcgaacaccctaactaacaatgttcttcttcatttcgatatatgagtcttaagctaaaactgtatacttgcgttgttggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC