Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 11
---------------------------------------------------------------------------------------------gtaaatcaatca--agtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgatt----ccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
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gtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttagGTTGGAGCTGAAATTGTAAGGAGAGCGCTGAGCTACCCGCTTAAATTGATTGCTAAGAATGCTGGTGTTAATGGAAGCGTTGTTACCGAGAAG
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------------------gtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG-------
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gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtca-tgacttcaaaattg-tgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------------------gtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
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gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtca-tgacttcaaaattg-tgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------------gtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
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gtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtca-tgacttcaaaattg-tgtttaatttttgcaggttggagCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------------------------------------------------gtaaatcaatcaagtcttcagattttaactc--atgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
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gtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATTGCCAAAAATGCTGGTGTTAATGGAAGTGTGGTCAGTGAGAAGMapped 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|125103079|gb|EL157610.1|EL157610EST: TTAAAGCCACGCTTGATAATGATGAAGAAAAG GTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATC
genomic: TTAAAGCCACGCTTGATAATGATGAAGAAAAGgtaaatcaat ... ttccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATC
EST:
gi|86087081|gb|DR382840.1|DR382840EST: TCCAAGGTTGATGCCATTAAAGCCMCGCTTGATAATGATGAAGAAAAG GTTGGAGCGGATATAGTTAAAAGAGCMCTAAGTTACCCCCTAAAACTAATC
genomic: TCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAGAAAAGgtaaatcaat ... ttccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
ttcccttt CT-rich tract
taacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcaatcaagtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttagGTTGGAGCGGATATAGTTAAAAGAGCACTAAGTTACCCCCTAAAACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG