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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag

Basic information

species Arabidopsis thaliana
transcript AT2G27530.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 3
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag-----------------
 ||||||||||||||||||||||||||||| ||| | || || || || ||||| || |||||| | || |||||||| ||||| ||||||||||| |||||  |  |    | |||   |||||  |    |   | || |  ||    |||||      |||  | ||   |||||  |||||                 
TCAAAAGGATAAGCGTTTCAGTGGATCTGTTAAGTTGCCTCACATCCCCCGCCCTAAGATGAAGGTGTGCATGCTTGGTGATGCCCAGCATGTTGAAGAGgtattgtactcttttatcagttttgcatcaacttccttgtgtacataacagattgtgctttagtaatagaaaattgtt--gataggcttctacaatgaaggg

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 5'ss of exon 3
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgt--ttgttttgatag----------------
 ||||||||||||||||||||||| ||||| ||||| || || || ||||| || ||  ||||| | || |||||||| ||||||||||| || || |||||   | |    ||||    |||||  |   |   |||||||  ||  | |||    | | |   |||   |   |||  | | ||                 
TCAAAAGGATAAGCGTTTCAGTGGTTCTGTTAAGCTGCCCCACATCCCTCGGCCTAAGTTGAAGGTTTGCATGCTTGGTGATGCTCAGCACGTCGAAGAGgtatgttatgcttctactgattttgcat---tgacttggttttgatatgagatgtggagagaacttttatcgcaattgggtagttactactacgtatttagca

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G023748_T02 (Zea mays), 5'ss of exon 3
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctata--ctttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag-------------
 |||||||| ||||| ||||| || ||||| ||||| || || || |||||||| || |||||| | || |||||||| |||||||||||||||||||||||   | |    || ||   ||  |  ||| | || |||||  | ||||        || ||     |    | |||| | |  |||             
TCAAAAGGACAAGCGCTTCAGCGGTTCTGTTAAGCTGCCTCACATCCCTCGCCCTAAGATGAAGGTTTGCATGCTTGGTGATGCTCAGCATGTTGAGGAGgtatgttatgcttccatcatctcgtcctgtgttttttttggcgtaaatttacttggtactcaggaattcaattatttgctcttgtagcgaatatgagctt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctat--------actttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag-------
 || ||||| |||||||||||||| ||||| ||| | || |||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||||| |    ||| | |          ||     |  |   | || || ||     |  |  | || |       || |||      |  |||         
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G37980.1 (Glycine max), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttt-tgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag-----------------
 || || ||||||||||||||||| ||||| ||||| || |||||||||||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||  |   | |||    ||| |  | | ||| |   ||   |  |||        ||||     ||||| |  |   ||||  ||                  
TCAGAAAGATAAGCGTTTCAGTGGTTCTGTTAAGCTTCCGCATATTCCTCGCCCTAAGATGAAAATCTGCATGCTCGGTGATGCTCAGCACGTTGAAGAGgt--tcatattcttctaactataatatatatatgcctttactataatattcatgcgaca-gttttgtttcaaatggatttttttaattcaagtttaaattttt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaag-----tgtttg-atgtttgttttgatag-----------
||| ||||| |||||||||||||| ||||| ||||| || || || |||||||| || ||||| || || |||||||| ||||||||||||||||| |||||   |  | |  | ||| |  |   |  |||| |    |   || |  |   ||| |   ||     || ||| |||||  |||| |  |           
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctct--atttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgt--------gattgaaatctctatactttttgtgta--tcttgtttggtttgaat----tggtgattgacacaaagtgtttgat--gtttgttttgatag
 || ||||| |||||||| ||||| ||||| ||| | || || ||||||||||| || |||||||| ||||||||||||||||| || || ||||| |||||        |||  || | || |  | || || |    | |   |||| |  |||    |  || || ||| |  ||||||| |   |||   || ||| 
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgtttgcttcctttccatttata-

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 3
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaat-ctctat--------actttttgtgtatcttgtttggtttga-attggtgattgacacaaagtgtttgatgtttgttttgatag------
||| ||||| |||||||||||||| || || ||| | || || || |||||||| || ||||| || || |||||||| ||||||||||||||||| |||||   | |  | | ||||        ||| ||| ||| |    |||  || |    ||  |     | | |||| |  ||  ||    |   |        
ACAGAAGGACAAGCGTTTCAGTGGCTCCGTCAAGTTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtatctaatttgccctattcatcgaaactctttatgt-tgccatttaattaggtgctgtagggaacccccaagtttaagaaattaacctcattgttatctt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G32330.1 (Glycine max), 5'ss of exon 1
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgt--------gattgaaatctctatactttttgtgta--tcttgtttggtttgaat----tggtgattgacacaaagtgtttgatgtttgtt--ttgatag
 || ||||| |||||||| ||||| ||||| ||| | |  || |||||| |||| || |||||||| ||||||||||||||||| || |||||||| |||||        |||  || | || |  | || ||||    | |   |||| |  |||    |  || ||  |  |  ||||||| |  || ||  || ||| 
TCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCGTCACATTCCTTGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACATGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgtgagattttcaattgggtgcaataatatattgctttgctgactgtgtttgcttctttttcatttata-

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 5'ss of exon 3
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtga---ttgacacaaagtgtttgatgtttgttttgatag-------------
 |||||||| |||||||| ||||| ||||||||||| ||||| || ||||| || || ||||||||||| |||||||| |||||||||||||| || ||||| | | |  | | |  |||| |     |  |   |  |    ||    | |   ||||     | |  |       | |||| ||               
CCAAAAGGACAAGCGTTTTAGTGGGTCTGTGAAGCTGCCACACATCCCTCGTCCTAAGATGAAGATCTGCATGCTTGGTGATGCTCAGCATGTGGAAGAGgtaaattac-tgttttgacttatctaacaaataactgagaacaaaacaataaaaattgattttgatttctcctatcattttttaatccttgattttcctgt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 5
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatct-ctatactttttgtgtatct-tgtttggtttgaa------------ttggtgattgacacaaagtgtttgatgtttgttttgatag-
 || ||||| |||||||||||||| ||||||||| | || || || |||||||| || |||||| |||| |||||||| |||||||| || || || ||||| ||||   ||  ||   ||   |   |  |  |    |   ||||            ||| | |||||   | | | ||  |   || ||||| |   
CCAGAAGGACAAGCGTTTCAGTGGTTCTGTGAAGTTGCCCCACATCCCTCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCTCAACACGTGGAAGAGgtaattgtgctccacttggctgcattaatggcaataaaagaagtgaaagacaagtgtcattgctaattgaagaatatttttcaactatttttttgtttaa

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgat--tgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaa--agtgtttgatgtttgttttgatag--------------
 || || || || |||||||| || ||||||||||| ||||| |||||||| || || ||||   | || |||||||||||||||||||| || |||||||| ||  |   |  |    |   ||| ||  |     || |||| | ||   ||||  |   |  | ||| | || | |      |                 
CCAGAAAGACAAACGTTTCAGCGGCTCTGTGAAGCTGCCACACATTCCTCGTCCTAAGATGAGAGTGTGCATGCTTGGAGATGCTCAGCACGTCGAGGAGgtcatattcgcacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatag

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtt-tgatgtttgttttgatag------------------------------------------------------------------------------------------------------------
 || || || |||||||||||||| || |||||||| || || |||||||| || || |||| ||| ||||||||||||||||| || ||| |||| |||||      | |||| |   ||  |   |    | | | | | |     |  ||||| | |||   || |    |||  |    | |                                                                                                            
CCAGAAAGACAAGCGTTTCAGTGGCTCCGTGAAGCTTCCCCACATTCCTCGTCCTAAGATGAGGATTTGTATGCTTGGAGATGCCCAACATATTGAAGAGgtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattga-ataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacag

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatact--ttttgtgtatcttg-------tttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag------------------
 || || || |||||||||||||| || |||||||| ||||| ||||||||||| || |||    | || ||||| |||||||| ||||| |||||||||||  ||    |  ||  |||  |       || |||       ||| ||  | || |     | || ||   || ||     || |||                        
CCAGAAAGACAAGCGTTTCAGTGGTTCCGTGAAGCTGCCACACATTCCTCGCCCTAAGATGCGCGTGTGCATGCTCGGAGATGCCCAGCACGTTGAGGAGgtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcat-gccacattacgcaggttgattacctcttatttattcgccccattattgcgtaacag

Mapped 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|86077209|gb|DR372966.1|DR372966
EST:     AAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
genomic: AAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
EST: gi|124764275|gb|EH854405.1|EH854405
EST:     GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACATG
genomic: GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACATG
EST: gi|164086393|gb|ES129330.1|ES129330
EST:     GCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
genomic: GCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
EST: gi|164077457|gb|ES116973.1|ES116973
EST:     GTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
genomic: GTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTT
EST: gi|164148908|gb|ES029402.1|ES029402
EST:     GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACA
genomic: GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACA
EST: gi|163981647|gb|ES037233.1|ES037233
EST:     GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACA
genomic: GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACA
EST: gi|164150054|gb|EL972739.1|EL972739
EST:     GCCC-AAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAG                         GCAGAGAAAATGGGACTTAGTAACA
genomic: GCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaa ... gttttgatagGCAGAGAAAATGGGACTTAGTAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG