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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag

Basic information

species Arabidopsis thaliana
transcript AT1G54270.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 3
GATGGACAGG-ATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
 |  ||  || | || ||||||||||||||||| || ||| |||| ||||||||||||||||| |||||||||||||||||  | || || |||||||| |||| ||   |     || |     | |  ||||   || | | |    ||   |   |   | |     | |||       |   ||| | |      | |        
-ACTGATGGGCAAGAATTCTTCACCTCATATGACGAAGTCTATGACAGCTTTGATGCCATGGGATTGCAAGAGAATCTTCTGCGAGGCATATATGCTTATGgtatgtactggcatattgatcc--ccatattttaaatgct-tatacatatctgttgcagtgtcaattgctctgcgagactttaaaattcagttaaaagtataa------

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G20300.2 (Glycine max), 5'ss of exon 3
GATGGACAGG-ATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag----
 |  ||  || | || ||||||||||| |||||||| ||  |||| ||||||||||| ||||| |||||||||||||||||  | || || |||||||| |||| ||   |     ||        | ||  || |||   |||||   |||| |||    |  |      ||||   || || |||  || |     |||   ||  |     
-ACTGATGGGCAAGAATTCTTCACCTCTTATGATGAAGTGTATGACAGCTTTGATGCAATGGGATTGCAAGAGAATCTTCTGCGAGGCATATATGCTTATGgtatgtactggcatattgtg-----atccccttattttaaatgttt--attcatatctgttaca------gtgccgattgctctgagagactttaaaattcagttaaaaatat

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaa---gaaggtttaaagaaacaacc-ttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   ||||| || |||   || || || || ||||| || ||   ||| ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| ||||||| ||  |     |  ||| ||   || |   ||||  || || | |  | | |    ||   | ||| || |  |||||          |||  | || ||||        
ACTGATGGGCAAGAT---TTTTTTACTTCTTATGACGAAGTTTGTGAAAGCTTTGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATACGgtatgttcattaatatatttgaatgtacgataattttagttcttgtttgagaactttagtt---tctattgttta-gctctgcatcaaatctga--gattaattta-------

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtg-aagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   |||||||||||    |||||||| || ||||| |||||  |||| || ||||| || ||||||||||| ||||||||||| ||||| || || || |||||||  |  || |   |||   |  |    |  ||| | ||| | |||   ||  || | | |  | |         |  |  |||  |  |    |||| | | |   ||
TCTGATGGACAGGAC---TTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTACGCATACGgtatttttaatattctttcttgggatttgccattggt-gttttattgt--tttttaatgaataaaccac-------caattttgtcctcaaactattgagtatctatcag

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G18760.1 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaa----acaacctttt-------gtttgttatgttgggattcctatta-actttatcgt-atgtgctctttcctgtgattgattggttgatttttttctag------------------------------------------------------------------------
   ||||||||||||   || ||||| || |||||||||||  |||| || |||||||| ||||| |||||||||||||| || || || || ||||| || ||||  |  |      || | |      |  || ||||       |||| | |      || |  | ||  | |||||||| |||     | |  | |   | ||| |||   |||||  | |                                                                        
TCTGATGGACAGGAT---TTTTTCACATCTTATGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttag

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag-aaggtttaaagaaacaacc-ttttgtttgttatgttgggattcctattaacttta-tcgtatgtgc-tctttcctgtgattgattggttgatttttttctag
   ||||| || |||   || || || || ||||| || ||   ||| ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| || |||| ||  |  ||  ||| ||   |||||  ||||   | || | |  | | |   |||    ||  |    | ||| ||   |||| |||| |||                 
ACTGATGGGCAAGAT---TTTTTTACTTCTTATGACGAAGTTTGTGAAAGCTTTGATGCTATGGGATTGCAGGAGAACCTTCTGAGGGGTATTTATGCATATGgtatgttcattaatattttaatttacaacaattttaaatcttgtttgagaaatttaatttctattggttaggtctgcatcaaacctgagattaatttaca-------------

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   ||||| ||||||   |||||||| || || ||||||||  |||| || |||||||| ||||| |||||||||||||| || || || || ||||| || ||||  |  |      || | |         ||| ||  || | ||    |||| |   |     |  | |||  | | || ||      ||||  | ||||||||    
TCCGATGGTCAGGAT---TTCTTCACATCCTACGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaactttctttatgtcctcttacttttttaattttatt----ttccaaaccaagagttattttgtattttatcgtgatgacaattg--taatttttttt---

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G03020.1 (Glycine max), 5'ss of exon 3
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag-aaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   |||||||| ||    || ||||| ||||||||||| ||| |||| || |||||||| |||||  | ||||| |||||||| || || || |||||||| |||| |  |||  | ||||           |||  |||  |||| |    |||  |    | |     | || ||||||||           |||        ||      
GCTGATGGACAAGA---ATTTTTCACTTCATATGATGAAGTCTATGATAGTTTTGATGCAATGGGCCTTCAAGAAAATCTTCTCAGAGGCATATATGCTTATGgtatgacaagtgatgtttcctttgtt--tcttcagttgcttattt---aattattgaggaatactaggaatatgctcttttaaacacactcttgacaacgggttc-----

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   ||||||||||||   |||||||| || |||||||||||  |||| || |||||| | ||||||||||||||||||||||| || || || ||||| || ||||    ||  | |||| || |        ||| |  ||| | ||   ||      | | |   |   || | ||   | |  ||||  ||   | | ||         
ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatct-cttgcttccatgatcaatcaatggttta--------

upper sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 2
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtga------agaaggtttaaagaaacaaccttttgtttgttatgttggg-attcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag
   |||||||| |||   |||||||| ||||||||||||||| |||| || |||||||| ||||| |||||||||||||| || || || || ||||| |||||||  | |      | |    || ||| |  ||   | ||| |||| | | ||  |   || || |    ||   |  ||    ||  |   |   | ||||  |           
ACTGATGGACAAGAT---TTCTTCACATCATATGATGAGGTCTATGAAAGTTTTGATGCAATGGGGTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATACGgtagtttacctttaatacctctttaagtaggaaa--tatgtctgttgtctaggatagctctcttgaggacattccacttgtcagttgattcaa---aatggtaaa-----------

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|124942045|gb|EL018346.1|EL018346
EST:     GGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTGCTATTCAGC
genomic: GGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGC
EST: gi|124909152|gb|EH983232.1|EH983232
EST:     CCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
genomic: CCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
EST: gi|125123678|gb|EL170076.1|EL170076
EST:     TTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
genomic: TTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
EST: gi|124837393|gb|EH921832.1|EH921832
EST:     TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTT
genomic: TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTT
EST: gi|124772951|gb|EH863080.1|EH863080
EST:     TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTAAGCTATTCAGCAAAGAGGAATTGTACCCTTT
genomic: TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCT--GCTATTCAGCAAAGAGGAATTGTACCCTTT
EST: gi|164030510|gb|ES139107.1|ES139107
EST:     GAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
genomic: GAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCA
EST: gi|163983032|gb|ES105910.1|ES105910
EST:     TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACG                         GTTTCGAAAAGCCTTCTGCT
genomic: TGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaag ... ttttttctagGTTTCGAAAAGCCTTCTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA