Sequence
atgc intronic sequence ATGC exonic sequence...actctctcaagtgtttgtttttacattcactgagcttcagattgctgcattacatgttgacgcaaaccaagtaagttactactcactttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g02470.1 (Oryza sativa), 3'ss of exon 3
--------actctctcaagtgtttgtttttacattcactgagct-tcagattgctgca--ttacatgttg-----------acgcaaaccaagtaagttactactcact---ttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
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gtctgtatgcttcgacgataatctgtttcttttgtttttggtctatcaaatcaatccaacttgcattttactcggtaaagaattcaaattgtaccagacataactaactctttcattttctgtagAACCCCAGCGTTTCTCAAAGGATGGGTATGAAGAACACATGCAAGTGAACCATCTTGCACCGGCTTTATTGGCAGTGTTGCTTCTACCTTCCCTTCTTCG
upper sequence: AT5G53090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G018251_T02 (Zea mays), 3'ss of exon 3
----------------actctctcaagtgtttgtttttacattcactgagcttcagattgctgcattacatgttgacgcaaaccaagt--aagttactactcactttgatt-tatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
| | | ||| ||| | ||| | || | |||| || | | |||||| |||| || || | | || || |||| ||| ||| ||||||||||| ||| |||| |||||||||||||||||||| | || || || | || | | || ||| | || || ||| ||||
gtctgcaggattattcattaacccaaccgttcggattttgacataccaaatctcaggtttcagttagacatgt-attttaaactgtaccagagctatcaaccttttcaatcctatgtagAACCCCAGCGTTTCTCAAAGGACGGACATGAAGAACACATGCAAGTGAACCATCTTGCACCTGCGTTACTGGCGATGCTGCTTATACCTTCCCTTCTCCG
upper sequence: AT5G53090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g00520.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------actctctcaagtgtttgtttttacattcactgagctt--cagattgctgcattacatgttgacgcaaaccaagtaagttactactcactttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
||| | || || | | || | | | | || || | | || || | | | | || | | | | | ||| ||| ||| || || |||||||| || ||||| |||||||||||||||| ||| | |||||||| |||||||| || | |||||||| || ||||| |
gttcttacatttttcattttatccagaattttgcatcttttgtgtattcatgtataatataaacaatgtgaatagttttttcccttctgatcaaacttgtagtacttcacttttttttttcccttttgtatttagAACCACAAAAATTTTCAAAGGACGGGTATGAAGAACACATGCAAGTGAATCATCTGGCTCCAGCATTGCTTTCAATATTGCTTTTGCCATCCCTTATTAG
upper sequence: AT5G53090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S100_75V6.1 (Physcomitrella patens), 3'ss of exon 3
----ac-tctctcaagtgtttgtttttacattcactgagcttcagattgctgcattacatgttgacgcaaaccaagtaagttactactcactttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
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ctacacatatctcgggatgatagattaac-tgtaccggttctcgaatgttcgaacctggt-ttgtcgtggtctgagt---tttcttctttggtgcgtggtcgcagATACAAAGAACTTGTCAAGGGATGGCTACGAGCATCACATGCAAGTGAACCATCTTGCCCCAGCTCTTTTATCGTTGTTGATGTTGCCGTCTTTGCTTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcattacatgttgacgcaaaccaagtaagttactactcactttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
tttgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actctctcaagtgtttgtttttacattcactgagcttcagattgctgcattacatgttgacgcaaaccaagtaagttactactcactttgatttatgcagAGGAACAGAAGTTCTCAAAGGATGGATATGAGCAACACATGCAAGTGAACCATTTAGCTCCAGCTCTGCTTTCACTACTCCTTTTGCCCTCACTTATCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- -ctctcaa
- - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacca