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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC

Basic information

species Arabidopsis thaliana
transcript AT3G47060.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
                         | | |  |  | | | | ||  | ||| |  || |||     || |||| | |  | ||  ||||| |       | || ||   ||| ||||| || ||||| ||||| || || || ||||||||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| ||| 
------------------------gtcagttctgcagt-catttaagtaatgatg-aatgttgctggactagagtttt--tgtactatgatgta------attcatta--tttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G072865_T05 (Zea mays), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagct-ctcctttagaatgatatgcctt-------tgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC------------
 |  || |      | |   ||    |  | |  ||||  ||   |        |   | ||| || |    | || || ||| | |||  | |   ||       ||      ||  | | ||||| |||||||| || || || || || ||||||||||| || || || || ||||| |||||||| ||||||||||||||||| ||||| ||||| ||||            
-ttcgtctcggtgctcgccctcctcgtggtgtcttattg-gttggttctgcaaat--gcttttagtaatggaaactactgcttgacaattgtgtttgttaccataatgtaattctttctctacaggtgggtcttccagggactggaaagacacttcttgcaaaagccgtagcaggagaagcagaagTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGCTATATGTAGGCA

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
                        ||  ||||   | | | | ||  | ||||   |||   || ||   |    | |   |||  || || |       | | |||||| | | |||| |||||||| || || || || || ||||||||||| || || || || ||||| |||||||| ||||||||||||||||| ||||| ||||| ||||
-----------------------gttggttctgcaaatgctttta-gtaatgga--aactactgcttgacaattgtgtttgttaccataatgt-------aattctttctctac-agGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCATTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
                         ||  | ||  |     |||   | ||||   ||    || ||   |    | |   |||  ||         |||      ||  | | ||||| |||||||| || || || || || ||||||||||| || || || || ||||| |||||||| ||||||||||||||||| ||||| ||||| ||||
------------------------gttggttttgcaaatgctatcagtaatggc--aattactgcttgacaattgtgtttgttaccata--------ttgttattctttatctacagGTGGGTCTTCCAGGGACTGGAAAGACACTTCTTGCAAAAGCCGTAGCAGGAGAAGCAGAAGTCCCGTTCATAAGTTGCTCTGCTAGTGAATTTGTTGAGC

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
          | |  || |||||||||  |||| |  | | | | |       |||||| ||   ||| |     | || | |||  |  |     | ||  |   || | || ||||| |||||||| |||||||| || ||  | ||||| |||||||| |||||||||||||| || || || |||||||| ||||| |||||||| |||||  
---------ttgaaatgttttcacttttgtctttt-ctgcatgtttgaggatttttaacattgttttata----ttgtcatctagg-tagtgaatatctg--ttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA0028S00210.2 (Glycine max), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
            |  || |||||||||  |||| |  | | | | |       |||||  ||   |||     | |  | | |||  || |     | |  ||   ||   || ||||| |||||||| || ||||| || ||  | |||||||||||||| |||||||||||||| || || || |||||||| ||||| |||||||| |||||  
-----------gaaatgttttcacttttgtctt-tgctgcatgtttgaggatttttaatattgtttta----ggttgacatctaggctg-tgaatatctctcttgattaccttacagGTGGGTCTTCCTGGCACAGGTAAGACTTTACTTGCAAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
gtgagttttatcatttgatttcactttattcttatattacgtatat----atcatggtttaacgtt-tggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
                     |||  | |   |  ||||  ||||      | |   ||| |  || |  ||     |  |   | |     |  ||    |   |||  ||| | || ||||| |||||||| || ||||| || ||  | || ||||||||||| || ||||||||||| || || || |||||||| ||||| ||||||||||||||| 
---------------------cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatcc-actgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 5
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
       | ||| | ||       |||||    |  |||| | |  ||  |   |||  ||||   |   | |      | |  | |  | ||  |    |||  ||| | || ||||| |||||||| || ||||| || ||  | || ||||||||||| || ||||||||||| || || || |||||||| ||||| ||||||||||||||| 
------ctcatcgtatgtggattatttatagccaagttactttttcatatta--ttattgttttaatttgaaa------cgtaggtagtaaatatcc---actgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT

upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
     |   |         | ||  |  ||   ||| |         || ||| |  | ||||   |  | | ||| |  |||  ||   || | ||||| ||      | || ||||| |||||||| || ||||| || || || || ||||||||||| |||||||| |||||||| || || |||||||| ||||||||||||||||||||  
----ctaccaaagaacagatacaagtggtttccataatttac-----tcttggatgtaagtttttatgtatg-gctttgatttgtaa--gtacggctttggct-----atcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT

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|124936215|gb|EL013137.1|EL013137
EST:     AAAAGTATGTCCGTCTAGGTGCACGTCCTCCGCGTGGTGTCCTATTG                         GTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGG
genomic: AAAAGTATGTCCGTCTAGGTGCACGTCCTCCGCGTGGTGTCCTATTGgtgagtttta ... tcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
                                 ctttgac  putative branch site (score: 4)
                              tgcctttgactccttt  CT-rich tract
                  tttagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG