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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag

Basic information

species Arabidopsis thaliana
transcript AT1G01050.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 5'ss of exon 4
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG-
|||||||||||||| || |||||||| || ||||| ||||||||||| || || ||||| || |||      |||  ||  | | || | ||  ||   |||    |         |||  ||| | |||| |  || | ||| |    | |  ||          
GTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttctatttgtaaaatgattgcttgcatatcattaccacaactctatttcaagaacaatatggactaatttcataattattttttgtgtactta

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 2
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgt-tagatgagaacaaagtt-----tatttttt-----atatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag
|| || |||||||| || || |||||||| || |||||||| ||||| ||||| || ||||||||||| |  | ||   ||| | |      ||||  |      | |  |     ||||         ||||    | | |  | ||||   ||||   |||
GTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAGgtctgcaagactgcaacgctgcacgcatttcctcccacgtctctaaaaacttctctcgattgcatcatgagcta-agatctgaaaaatctcggacag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G104918_T03 (Zea mays), 5'ss of exon 4
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgt-taga---tgagaacaaagtttatt--ttttatatgaatggttt---tcttatagcaaaatcaatctcaacaagtttgaatt-ctctcattcag----
|||||||||||||| || |||||||| |||||||||||||||||||| || || ||||| || ||||| ||     ||    ||| |||||||   | | |||||    |||   ||| |    | | |    |  ||  ||  || ||| ||   | |       
GTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAGgtatatgctctgctctcaatgtttattacatctttatgaccactttctgtctcaataaacagtatggcataagcagcatgtatttcttgtacttgtgcaa

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G061928_T02 (Zea mays), 5'ss of exon 4
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgt-tagat---gagaacaaagtttattttttatatgaatggttttct-tatagcaaaatcaatct----caacaagtttg-aattctctcattcag-----
|||||||||||||| || |||||||| || ||||| ||||||||||| || || ||||| || ||||| ||  |   |    ||| |||| ||   | | |||       ||| ||||  || | || | |     ||| ||  || | ||||   |||        
GTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtatatgttctgttgtcaatgtttcttacatct-tgatcaccactctctatattaataacagtatgggataaccagcatgcagttcttgtatttgtgcaat

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G42280.1 (Glycine max), 5'ss of exon 4
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatggttttcttatagcaaaatca----atctcaacaagtttgaattctctcattcag--------------------
||||| ||||||||||||||||||||||||||||| || |||||||| ||||||||| | || |||||   |    ||     |   | ||  |  ||||   | | ||||  || |||| |     |  | | |    |  ||  |     | |                     
GTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAGgtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G05390.1 (Glycine max), 5'ss of exon 4
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatg-gttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag--------------
||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||| | || |||||  ||    |       ||  |||| | |||   |  | | | |||   |  |  ||  |  ||| |             |  |||              
GTTGTGGAGATCACTAAGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaaccaattgcttcttcgttttgaaatgggagtatctacctatga-agcacgaactttgacacggacaccggacacgacacagacatggacacttcg

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G45050.1 (Glycine max), 5'ss of exon 3
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttata-tgaatggttttcttatagcaaaatcaa------tctcaacaagtttgaattctctcattcag------------------------------------
||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||| | || |||||   |  |    |  |  |  ||  | || || | |   ||  |   | |   | ||      | || | | | ||   |||    |  ||                                     
GTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAGgt---acaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G18510.1 (Glycine max), 5'ss of exon 3
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatggttttcttatagca-----aaatcaatct--caacaagtttgaattctctcattcag------------------------------------
|||||  |||||||||||||||||||||| || || || |||||||||||||| ||| | || |||||   |    |  |    |  ||  |   ||| | |    |  |     |     |||  ||| |  ||     |||     | |  |  ||                                     
GTTGTGCAGATCACTAAAGGAAGCAAGGTTAAGTATGAACTTGACAAAAAGACTGGATTGATTAAGgtacaaaccaattac--ctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G16860.1 (Glycine max), 5'ss of exon 1
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatggttttcttatagca-----aaatcaatctcaacaagtttgaattctctcattcag------------------------------------
||||| ||||||||||||||||||||||| || || || |||||||||| ||| ||| | || |||||   |    |       |  ||  |   ||||| |    |  |   | |     ||||  || ||    |   |   | | |  |  ||                                     
GTTGTGGAGATCACTAAAGGAAGCAAGGTTAAGTATGAACTTGACAAAAGGACTGGATTGATTAAGgtacaaaccaattgc--ctggttactggaatgaaagcccctactgctgtagcttgaaatagatttcccagatgatttttccccatacccatctatctttatgcttacgattttcgaataattcacag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA11G18100.1 (Glycine max), 5'ss of exon 3
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgt-tagatgagaacaaagtttattttttatatgaatggtt-ttcttatagc--aaaatcaatctcaacaagtttgaattctctcattcag--------------------------------------
||||| ||||||||||||||||||||||| |  || || |||||| ||||||  ||| | || |||||  | |  |       | ||| |    ||   |     |  |  | ||||   ||||  || ||    |   |   ||  ||||| ||                                       
GTTGTGGAGATCACTAAAGGAAGCAAGGTTATGTATGAACTTGACCAAAAGATTGGATTGATTAAGgtacaaaccaattgcctggttactgga-atggaagcacctactgctgtagcttgaaatagatttcccagatgatttttttcctcatacacatctatctttatgcttacaatttccgaataattcacag

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ33440 (Selaginella moellendorffii), 5'ss of exon 3
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagat-gagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag
||||| |||||||  |||||| |||| || ||||||||||| ||||| ||||  || |||||||||||| ||| ||| | ||     |||||  |||    |  ||||   |  ||  |                                  
GTTGTGGAGATCAGCAAAGGAGGCAAAGTGAAATACGAGCTGGACAAGAAGAGTGGTCTCATCAAGgtttgattgaggagaacaaacattttggatacttcttattttaaaactgcgcag---------------------------------

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ27219 (Selaginella moellendorffii), 5'ss of exon 3
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagat-gagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag
||||| |||||||  |||||| |||| || ||||||||||| ||||| ||||  || |||||||||||| ||| ||| | ||     |||||  |||    |  ||||   |  ||  |                                  
GTTGTGGAGATCAGCAAAGGAGGCAAAGTGAAATACGAGCTGGACAAGAAGAGTGGTCTCATCAAGgtttgattgaggagaacaaacattttggatacttcttatttttaaactgcgcag---------------------------------

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|164011430|gb|ES013757.1|ES013757
EST:     AAGGAAGCAAGGTCAAATACAAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCC
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCC
EST: gi|152033655|gb|BP561551.2|BP561551
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
EST: gi|86084748|gb|DR380507.1|DR380507
EST:     GACTCATCAAG                         G-TGATCGTA-TCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
genomic: GACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
EST: gi|125127475|gb|EL172292.1|EL172292
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTA
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTA
EST: gi|124920473|gb|EH994184.1|EH994184
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTACACAA
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCT-CACAA
EST: gi|47828474|gb|CK118158.1|CK118158
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
EST: gi|124751380|gb|EH841510.1|EH841510
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCT
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCT
EST: gi|124779662|gb|EH869605.1|EH869605
EST:     ACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTAACCCTCACAACTATGGTTT
genomic: ACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTA-CCCTCACAACTATGGTTT
EST: gi|124761394|gb|EH851524.1|EH851524
EST:     CAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
genomic: CAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
EST: gi|164215294|gb|ES070901.1|ES070901
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTT
EST: gi|125231155|gb|EL245240.1|EL245240
EST:     AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG                         GTTGATCGTATTCTCTACTCAT
genomic: AAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgag ... tctcattcagGTTGATCGTATTCTCTACTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAGgttagatgagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcag

- - - - - - - - AAGGAA
- - - - - - - - - - AAGCAA
- - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - GAGCTT