Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttgatcataaatcaggatttcaagttttaaagtcttttttttttctgaatctaaacaagtgttctctttgtcttcttcttgagagctaatgttgttggaagattgatttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61430.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G33270.1 (Glycine max), 3'ss of exon 1
---------------------------------------------gtatgttttgatcataaatcaggatttcaagttttaaagtcttttttttttctgaatc----taaacaagtgttctctttgtcttcttcttgagagctaatgttgttggaagattg-----atttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
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gtaagttcaaaacaaaatgaaaaaattcagccccactttggttttggttatttggcttctaaatatgttgtcttacaatgagaccatacggacagattcgatcccgatacaaaaacattctaaatatattgattgtgtaagtttattataactttatgttgtgtgcattttttttgggatacagGGAAAGCTAAAATGGGAGAGAAAGAGTGGTACTTTTTCTGTGTGAGAGACAGAAAATACCCAACTGGTTTGAGGACTAATAGAGCCACTCAATCAGGATA
upper sequence: AT5G61430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G21020.1 (Glycine max), 3'ss of exon 1
------------------------gtatgttttgatcataaatcaggatt-tcaagttttaaagtcttttttttttctgaatctaaac-----------aagtgttctctttgtctt--cttcttgagagctaatgttgt-tggaagattgatttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
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gtaagttcaaaacaaaattaaaaaattcagccccactttggttttggtttatttggcttctaaatatatttttgtcttacaacgagaccatacagactcaaatatattaattgtgtaagtttattataacattatgttgtgtgcatgttttttattttttgggttacagGGAAGGCCAAAATGGGAGAGAAAGAGTGGTACTTTTTCTGTGTGAGGGACAGAAAATACCCAACTGGTTTGAGGACTAATAGAGCCACTGAATCAGGATA
upper sequence: AT5G61430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G00930.1 (Glycine max), 3'ss of exon 1
gtatgttttgatcataaatcaggatttcaagttttaaagtcttttttttttctgaatctaaacaagtgttctctttgtcttcttcttg----agagctaatgttgttggaagattgatttttt---tgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA------
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-----------------------------------------------gtaagtgaaaccaaaccaattcgatcaatctacctttcatgtattatattgattttccttgaaaagttaaaattgcaagtttgtgtttagggaaagCCAAAATGGGAGAAAAAGAGTGGTACTTTTTCTGTGTGAGAGACAGAAAATACCCCACTGGCTTGAGAACCAACAGGGCCACAGAAGCTGGGTACTGGAA
upper sequence: AT5G61430.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G10970.1 (Glycine max), 3'ss of exon 1
gtatgttttgatcataaatcaggatttcaagttttaaagtcttttttttttctgaatctaaacaagtgttctctttgtcttcttcttgagagctaatgttgttggaagattgatttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
||| | | | || | | || | | || | | | ||| | || | | |||| | | |||| || | ||| || || | |||||| || |||||||| || || || ||||| ||||||||||||||||||||||| || ||||| || || ||||| ||| | || || ||||| || ||
-------------gtaagt--gaaaccaaaccaatccaatcaatctcacttttatgtat-------tgtattgcttttaattttctccaaaattaatattat---------gatctt-----gtgtgtagGGAAAGCCAAAATGGGAGAAAAGGAGTGGTACTTTTTCTGTGTGAGAGACAGAAAATACCCCACTGGCTTGAGAACCAACAGGGCCACCGAAGCTGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcttcttcttgagagctaatgttgttggaagattgatttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
tttttttgt CT-rich tract
attgatttttttgtgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttgatcataaatcaggatttcaagttttaaagtcttttttttttctgaatctaaacaagtgttctctttgtcttcttcttgagagctaatgttgttggaagattgatttttttgtgtatatagGGATGGCAAAAATGGGTGAGAAAGAATGGTATTTTTTCTGTGTGAGAGACAGAAAGTATCCCACCGGTTTAAGAACTAACCGAGCAACTGAAGCCGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC