Sequence
atgc intronic sequence ATGC exonic sequencegtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgataacgacttgtttcaaaaaacttcatacgagtcatatttcctttccttttgttattgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66250.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66250.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G05520.1 (Glycine max), 3'ss of exon 2
gtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgataacgacttgtttcaaaaaacttcatacgagtcatatttcctttccttttgttattgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
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------------------------------------------cgcatt-ttcttg-----ctaatggggtttaatttttaatttcaattctcatgtagtaggtttttt--ttttcttatt-taaaactagagatgtatttgtcttga----gcagGCTAGTTGGAAAGACTACCCAATTGGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTGAGGTTGAGTGCTCTGCTT
upper sequence: AT5G66250.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G08100.1 (Glycine max), 3'ss of exon 2
gtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgata--acgacttgtttcaaaaaacttcatacgagtcatatttcctt-tccttttgttattgtaagtttatgggaatgtc-aatgatgat--gaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
| || || | | | | |||||| ||| | | || || || | | | || ||| ||| || | | || | |||| | | | | |||||| ||||||||||| || || || || | |||||| |||||||||| || || ||||||||||| |||||||||||||| || ||| || || |
------------------------------------------------------ggttgcatggtgtgaacattcatttcaa-----ttctcatgttcaatgttcatttctacctctgatatcgta--cttgtctaattgactaatgttcctttggagcagGCTAGTTGCAAAGACTACTCAATTAGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTTAGGTTGAGTGCACTGCTT
upper sequence: AT5G66250.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G37180.1 (Glycine max), 3'ss of exon 2
gtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgataacgacttgtttcaaaaaacttcatacgagtcatatttcctttccttttgttat-tgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
| | | || | || | || || ||| | | || || || | | || | || | || || | | || | |||||| ||||||||||| || || || || | |||||| |||||||||| || || ||||||||||| |||||||||||||| || ||| || || |
----------------------------------------------------gtggtagcatggtgtgaacattcttttcaa---ttctcatgtacaatgttcatttctacctcgatacgtacttgtcttattgactgatgttcctt-tggagcagGCTAGTTGCAAAGACTACTCAATTAGAGGGTGAGAAAATGCAGAAAGAGGCTGAAGTTCAGAAACTTATGGAAGAGAATGTCAGGTTGAATGCACTGCTT
upper sequence: AT5G66250.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G23960.1 (Glycine max), 3'ss of exon 2
gtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgataacgacttgtttcaaaaaacttcatacgagtcatatttcctttccttttgttattgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
| || || || |||| ||| | || | || |||| | | | | | || ||||| | | ||| ||| |||| | | |||| | |||| |||||| || || |||||| | |||||| |||||||||| || || || |||||||| |||||||||||||| || ||| ||||| |
---------------------------------------acattttcttgcctatggggtttaatatttaatttt------aattctcatgcagttggtttatttatttcttttttaaaactaaag--atgcatttgtc--------ttgagcagGTTAGTTGGAAAGACTACCCAATTGGAAGGTGAGAAAATGCAGAAAGAGGCTGAAGTACAGAAACTTATGGAAGAGAATGTGAGGTTGAGTGCTCTGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcctttccttttgttattgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
ttattgtaagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcacccttgggatgagagatgagtgggattttcatcaggtttacactattcttaggtgtttgataacgacttgtttcaaaaaacttcatacgagtcatatttcctttccttttgttattgtaagtttatgggaatgtcaatgatgatgaaacagGCTTGTTGCAAAGACAACGCAGTTGGAAAGCGAGAAAGTGCAGAAAGAAGCAGAGGTTCAGAAACTAATGGAAGAGAATGTAAGACTGACGGCTCTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA