Sequence
atgc intronic sequence ATGC exonic sequenceGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctga--ggcttgaga-------agcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag-------------------------------------------------------
|| ||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || ||||| | | ||| || | | | |||||| || | | ||||| | | ||| | || ||| | || | ||
GTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAGgttagtctgttgttataactgctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgttgctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttgtcag
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgatttt-----gtattt---ctgaggcttgagaagcgtgttatttgcat--actcgtgaactataactaatcaggattttaattcttcag--------
|| ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| | || ||| || || | ||| | || | || | | | ||||| | | ||| || | |
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAGgtaagttgtcgaagtaattaacttgtgctgccagatttatatttctcatatttaattcacatgtataatgatatatgatgttggatgaaaaaattataga
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 4
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgatttt-----gtatttctgaggcttgagaagcgtgttatttgcatact-cgtgaactataact-----aatcaggattttaa---ttcttcag-----------------------------------------------------
|| ||||||||||| || || ||||| |||||||||||||| |||||||| ||||| || |||||||| ||||| | || ||| || ||| | || | | | | | || | ||| ||| | ||||| | | | || |||
GTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAGgtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatag
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| ||||||||| || | |||| | || | | || | || | ||| | | | ||| |
GTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAGgtgtccttttctttcccaaagtttttagattttttgggattctgtctgtaagctaatagtttgttgactttcag--------
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| |||||||| || | |||| | || | | || ||| || || | || ||| | || | || | | |||||
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttctt--ttgaattctgttt--ctgtaagctaatagtttgttgact-ttcag
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcg---tgttatttgc--atactcgtgaactataactaatcaggattttaattcttcag------------------------
||||||||||||||||||||||| || ||||| ||||| ||||||| ||||| ||||| |||||||| ||||| |||| || ||| | | | | || || |||| ||| || || || | | | || ||| ||
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgtaatttct--ttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
||||| |||||||||||||||||||| ||||| |||||||| ||||| ||||||||| | |||||||| ||||| | || || || || || | ||| | | | | | || | |
GTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGgtaa----atagatcggattctggaatattgtggtgtaagtgtt----taaattgcag------------------------
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: EFJ33580 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
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GTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAGgtaa----atagattggattctggaatattgtggtgtaagtgtt----taaattgcag------------------------Mapped 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|125282619|gb|EL296704.1|EL296704EST: GAGTTGAAGATGCTCTTAATGCAACAAAG GCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACT
genomic: GAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgt ... aattcttcagGCCGCTGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag
- - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGATG