Sequence
atgc intronic sequence ATGC exonic sequencegttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------gttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
||| | |||| |||| | | | | | || | ||| | |||||| || ||||||| || | ||||| |||||||||| ||||| ||||||||||||| ||||||||||||||||| ||||| || | |||||| || | |
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttat-aaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaata--tgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33390.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------gttcggtttttattaaaccaaaccggacttaac--cgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
| | | | ||| | |||| || | | | || | ||| | |||||| || ||||||| || | ||||| |||||||||| ||||| |||| |||||||| ||||||||||||||||| ||||| || | |||||| | | |
gtacactcaagcttcttcccatcttcaaaacagccatatcatgttacatatgcatatgcttataaacaaccactttttattgcatactttcaagttcaactaatgatgaaaccaaata--tgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTCAGAGGAAGGTTTGCAAAGAATGATGACTTTGGGGAAACCAATAGAACTACAAGTAGCA
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G21380.1 (Glycine max), 3'ss of exon 4
--------------------------------gttcggtttttattaaacca----aaccggacttaaccgttgt---------taaatgttgtcccaatg-atttttttggggg--gttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
|| ||| || || | || | | | || | | ||| | | || || | || || | | | ||||| |||||| || | ||||| ||||| ||||| || || | ||||||||||| ||||||||||||||||| ||||| |
aaaggatctcgaaattaatggtttggatagaagtatggtacttgatagaacattatggcggaagttgatccatgtagccgaccccacctagtgggataagGCGTTGTTGTTGTTGTTGTTGTTGTATGCTTGCCGCAAAACTTTGGCGGATAGCCGGCCCCGGGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAG------------------------
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G26990.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gttcggtttttattaaaccaaaccggacttaaccgt-tgttaaatgttgtcccaatgat------ttttttggggggt---tgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
|| | |||| | ||| | | ||| | | | || || || | |||||| |||||| || ||||||| || | ||||| || |||||||| || || | ||||||||||| ||||||||||||||||| ||||| ||| ||||||||| | |
gtactacatctgaacaccaacattaacaaacaaatttgaaatcttatattatgttatacatgatttccaatctattgcatcaatcaagccttgtgcatattttcaaaattcaactaatgatccaatgttttttaaaaaaaaaatgcagTATGCTTGCCGCAAAACTTTAGCAGATAGCCGGCCCCGGGTTAGAGGAAGGTTTGCAAAGAATGATGAGTTTGGAGAGAGCCATAGACAAGGAAGTAGCA
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0049g01830.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------gttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
|| | | || || |||| | || ||| ||| || || | | || ||||||| ||| | || ||| ||||||| || ||||| ||||||||||||||||||| || |||||||| ||||| ||| | |||| | | |
gttatctctctctctctcgttcttctgctatcattttacattcagatcatgtataggcatacgtatgataacttaaactttatt-ttcttactaaatgttagaaaaatataataataataatgcagTATGCATGTCGCAAGACACTGGCAGACAGCAGACCACGAGTTAGAGGAAGATTTGCCAAAAATGATGACTTTGGAGAGGCCCCTAGAGCCAGTGGTGGAC
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S143_20V6.1 (Physcomitrella patens), 3'ss of exon 4
-gttcggtttttattaaaccaa----accgga----------cttaaccgttgttaaatgttg------tcccaatgatttttttggggggttgt---agTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA------
| | || | | || | ||| | || | | | || | | | | || |||||| | |||| ||||||| ||| | ||||||||||||||||||||||| ||||| |||| | ||||||||||| ||| || | ||| | ||| ||| | |
tatctgattctcagtagagcaactgcatgagaaggtgattatttcagtgggtgccgagctctaatcgtttttgactgtttttttcgcaatattgtttcagTATGCCTGTCGCAAAACATTGGCAGATAGTCGACCTCGAGTTCGAGGGCGTTTTGCAAAGAAC-ATGGAT--GATGATTTA--CCGACC-GCTCTCCTAGGGCGCA
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S8_144V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------gttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaat---gatttttttggggggttgt---agTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA-----
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ggccacagcgatttcaagaagaaaaaacaattctctgatcaaatc---ctcagtgaatgttaaacaataacccattcttggtctttatgcaatgctcctccagTACGCCTGCCGCAAAACATTGGCAGATAGTCGCCCAAGAGTTCGAGGTCGTTTTGCAAAGAAT-ATGGAT--GATGAG--ATGCCGACCACTCTCCTTGGACGTAMapped 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|116378841|gb|EG421433.1|EG421433EST: GTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAG TATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGA
genomic: GTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttt ... ggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
acttaac putative branch site (score: 3)
aatgattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT