Sequence
atgc intronic sequence ATGC exonic sequenceCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23190.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 10
---CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagta-taccaagtacttttaaacttaaagtatctcttcatttgtag
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TTGACCGGATGGGCCTTGGAAAATCCTCAAATGC---TGAACCCCCAGAATTTGGTGCTGCAGCTGATGGTGATGCTGATCGCAACATGATTCTGGGTAAAAGgtattcttcagcctagatagcttgaagtttttgtatatactcataagtgctatgagaaattta---tgatgtgtcctttgccttctag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 10
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgta------gcttactgacgttttcaagagagatacatccatggaact---agta--taccaagtacttttaaacttaaagtatctcttcatttgtag
||| ||||| | || || || | | | ||||||||| || ||||| || || |||||||| ||||| ||||| |||||||| || ||||||||||| | | | || | | | | | | | | | || || | | | | | | | | | ||| |||
AACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTGGGTAAAAGgtatgatctgttcgagtatcttattatgtagaaagtttgttttggattctagataagcacaaggaattcatgatgcttcccctttgccgtgtttatag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgta--gcttactgacgt------tttcaagagagatacatccatggaactagtatac--caagtacttttaaacttaaagtatctcttcatttgtag
||| ||||| | || || || | | | ||| ||||| || ||||| || || |||||||| ||||| ||||| |||||||| |||||||||||||| | | || ||| | || | | |||| | | |||| | || || | | | | |||
AACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgct-atag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 10
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
| || |||||||| || |||||||| | || ||| || ||||||||||| || ||| |||||||||||||||| || |||||||| ||||||||||||||| | || | || | | | | || | | | || | | ||| | ||||| | | || |||
CTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtag--tgttgcc--cttaatttgtggtgaatttaaatattctcca-actttttgtgtgtaatatctgtgtatcccctgtttgttag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 3
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
| || |||||||| || ||||| || | || ||| || ||||||||||| || ||| |||||||||||||||| || |||||| | ||||||||||||||| | || | || | | ||| || | | | || | | | ||| | ||||| ||| || |||
CTCGTATGGGATTGGGCAAATCTGAACCCCAAGATGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtag--tgttgtc--cttaatttgtgatgaatttaaatattc--tctaacttttttgtgtaatatctgtgtatcccttgtttgttag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 10
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
| || |||||||| || |||||||| | || || || ||||||||||| || ||| |||||||||||||||| || |||||| | ||||||||||||||| | || | || | | ||| || | | | || | | | ||| | ||||| | | || |||
CTCGTATGGGATTGGGCAAATCCGAACCCCAAGAAGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtag--tgttgtc--cttaatttgtgatgaatttaaatattc--tctaacttttttgtgtaatatctgtgtatcccctgtttgttag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagc-ttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
|| | |||||||| |||||||| || || | ||| || ||||||||||| |||||| |||||||||||||||| ||||||||||||||||| ||||||||| | | |||| || ||| | | || | | ||| ||| | || | | || || | || | ||
CATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactgcacttcatttctggaaaga-atacttatt-atttgacata---agtcttaaatcacctgatttacct-tgcaatgtcag
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S4_12V6.2 (Physcomitrella patens), 5'ss of exon 11
--CACGA-ATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagaga-----tacatccatggaactagtataccaagt-acttttaaacttaaagtatctcttcatttgtag-------
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TGCAAGTTATGGGATTGGGCAAGACTCAACCTGA---CGAGATTCCGGAATTCGGTGCCGCTGCTGATGGTGATGCTGACCGAAACATGATTTTGGGCAAGAAgtatgtgatcagggctcccatctacgactccttgtcttaatctatctggaagttgatgtgatttctgtattcctgatcccgctaattctgtgttagctttMapped 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|47831641|gb|CK121325.1|CK121325EST: GGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAG GTTCTTTGTAACTCCTTCGGATTCAGTTGCCATAATTGCTGCANATGCTAT
genomic: GGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttact ... tcatttgtagGTTCTTTGTAACTCCTTCGGATTCAGTTGCCATAATTGCTGCAAATGCTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGTAACATGATCCTTGGTAAAAGgtagcttactgacgttttcaagagagatacatccatggaactagtataccaagtacttttaaacttaaagtatctcttcatttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT