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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag

Basic information

species Arabidopsis thaliana
transcript AT2G27530.1
intron # 5
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 5
lower sequence: LOC_Os02g21660.1 (Oryza sativa), 5'ss of exon 5
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtat--gattctgttttgttcctatgattg-tgtctaatttcttt-----ctaaatctctctctagt-gtactaat--tttga-------tttggatcttgatgcag
||||||||| |||  | | ||||| ||||||||| ||||||| |||||||||||||| || |||||||| || || || ||||||||||||||||| |||||||  |||  ||| ||  |  ||  || | |    ||||| | |      |  |  ||   |||||  | || ||  |||||       |||| ||| |  |||||
TGCTGTTGGCAACTGTGCTATGGAGGAGAAGCAGATCTTCCAAAATGTGCAGATGAGCGTGAACTTCCTTGTTTCCCTTTTGAAGAAGAATTGGCAGAACgtatgtgatcatgtgttccttatagcatagatacaaaatttatctgccacttggacatcagcctagttattctgatgatttgacatgttatttgtatcatcgtgcag

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g64090.1 (Oryza sativa), 5'ss of exon 5
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgta--tgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtacta-attttgatttggatcttgatgcag--------
|||||| || |||  | | ||||| ||||||||  | ||||| |||||||| ||||| || |||||||| ||||| || ||||||||||||||||| ||||||  |  | |  | || |   ||| |    |  ||  | |    |  ||||    |   |||   | ||| | | ||| || |   | |          
TGCTGTAGGCAACTGTGCTATGGAGGAGAAGCAAATTTTCCAAAATGTGCAAATGAGCGTGAACTTCCTTGTCTCTCTTTTGAAGAAGAATTGGCAGAACgtaagtactccaatattttctttataacacggagtacatgcaacatttatctactccctttgtttcatattataagttgcatttacttcctttacttttt

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G023748_T02 (Zea mays), 5'ss of exon 5
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag
||||||||| |||     |||||| ||||||||| |||||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||||| || ||||| | ||    | |   ||  |||    || || |  |   | ||  || || | ||  |||| | | || | | | |   |||||
TGCTGTTGGCAACTGCGGCATGGATGAGAAGCAGATCTTCCAGAATGTGCAAATGAGTGTCAACTTCCTCGTGTCGCTCTTGAAAAAGAATTGGCAGAATgtatgttcctcacatctgtataaaattaatgcttatgttctaaaatatgactatccactgggctaactgtcatcttg-tgtgtttgcag

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G31040.1 (Glycine max), 5'ss of exon 5
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgta--tgattctgttttgttcct-------atgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag---
 || || || ||  ||  |||||| || |||||  ||||||| ||||| ||  |||||||||||||||| |||||  | ||||| ||||||||||| |||||   |  | |  | ||     |       ||  |||  |||||     || ||  | | | | |  | |   | || ||||||  |  ||  |||     
AGCCGTGGGGAATGTTAGCATGGAGGAAAAGCAAATCTTCCAAAATGTACAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAATTGGCAGAACgtgagtagtccactcttaaaattgaataaaattgttgcatctaagcctattttac-tgtatttttgtttttgaagttatgatttcaaattttttgctctat

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 8
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgt-tttgttcctatgattgtgtctaatttctttc-taaatctctctctagt--gtactaa---ttttgatttggatcttgatgcag----
|||||| ||||||      ||||| ||||||||| |||| || ||||||||  |||| ||||| ||||| |||||  | ||||||||||| |||||||| ||  | |  |    ||    || | | | | |  || |       ||  |     |  |||   || |||   | |  ||  |  | | | | |      
TGCTGTGGGTAACTGCAGTATGGAGGAGAAGCAGATCTTTCAAAATGTGCAACTGAGCGTTAATTTCCTTGTCTCCTTGTTGAAGAAGAACTGGCAAAATgtgagttgattcacttagctctgttagtttatggaactaaaccaataggttatgataaagtttatattaaggctctcaatcagtctttaggtacctcact

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0007g03340.t01 (Vitis vinifera), 5'ss of exon 5
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgatt--ctgttttgttcctatgatt-----gtgtctaatttctttctaaatctc-tctctagtgtactaattttgatttggatcttgatgcag---
|||||| || |||     |||||| ||||||||| ||||||||||||||||  | ||||| |||||||| |||||  | |||||||| ||||||||||| ||| | |   |    |      ||  ||      |   ||||    |   ||  ||   |   | |   | ||   || |  || ||    ||| |    
TGCTGTGGGCAACTGCAGCATGGAGGAGAAGCAGATCTTCCAGAATGTGCAACTTAGTGTCAACTTCCTTGTCTCATTATTGAAGAAAAATTGGCAAAATgtaagttcagcaacctcacatttaacatgacaaagcagctaaccattaagtaggtcctatgctttgaaaattagggttcaactgcatgactatgtaccct

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 3
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag
 || || || ||| |    ||||| ||||||||| |||||||||| || ||| | || ||||||||||||||||||||  | |||||||| |||||||||||| |     ||   | | || |  ||     |   ||   |   |   |   || ||                               
AGCGGTGGGCAACATCGAGATGGAGGAGAAGCAGGTCTTCCAGAACGTTCAGCTCAGCGTTAACTTCCTCGTCTCGCTGCTCAAGAAGAACTGGCAAAACgtaagtagtagtagcgcttctctcttttctcgtggcttaacttcga--ttgattccag-------------------------------

upper sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 3
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag
 || || || ||| |    ||||| ||||||||| |||||||||| || ||| | || ||||||||||||||||||||  | |||||||| ||||| |||||| |     |    | | || |  ||     |   ||   |   |   | | || ||                               
AGCAGTGGGCAACATCGAGATGGAGGAGAAGCAGGTCTTCCAGAACGTTCAGCTCAGCGTTAACTTCCTCGTCTCGCTGCTCAAGAAGAACTGGCAGAACgtaagtagtaggagcgcttctctcttttctcgtggcttaacttcga--ttgtttccag-------------------------------

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|164225510|gb|ES011230.1|ES011230
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTG
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTG
EST: gi|125206189|gb|EL221143.1|EL221143
EST:     GATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
genomic: GATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
EST: gi|164105495|gb|ES087576.1|ES087576
EST:     GTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAA
genomic: GTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAA
EST: gi|164016209|gb|EL989995.1|EL989995
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTA-GGTGTTTG
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTG
EST: gi|164128706|gb|ES152130.1|ES152130
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACC
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACC
EST: gi|86077209|gb|DR372966.1|DR372966
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
EST: gi|164153520|gb|ES039463.1|ES039463
EST:     AGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
genomic: AGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
EST: gi|124966685|gb|EL040773.1|EL040773
EST:     CCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATACTT
genomic: CCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAAT-CTT
EST: gi|124921341|gb|EH994967.1|EH994967
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACA
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACA
EST: gi|164126434|gb|ES008275.1|ES008275
EST:     ACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
genomic: ACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
EST: gi|124783095|gb|EH872985.1|EH872985
EST:     ATTGGCAAAAC                         GTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
genomic: ATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACTTGAAGAGCACCATGGGACCACCACAAAGAATCTTT
EST: gi|164025674|gb|ES033152.1|ES033152
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTG
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTG
EST: gi|164230110|gb|ES086195.1|ES086195
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTACT
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTACT
EST: gi|163997893|gb|ES102293.1|ES102293
EST:     AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAAC                         GTAAGGTGTTTGTAC
genomic: AGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattct ... cttgatgcagGTAAGGTGTTTGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGTTGGTAACCTTTCCATGGAAGAGAAGCAGCTCTTCCAGAATGTGCAGATGAGTGTTAACTTCCTCGTCTCGCTCTTGAAGAAGAATTGGCAAAACgtatgattctgttttgttcctatgattgtgtctaatttctttctaaatctctctctagtgtactaattttgatttggatcttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG