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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

Basic information

species Arabidopsis thaliana
transcript AT5G28050.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 3
gtaagatgtcga-aacaagtctactcacaaacccatc-----tttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
||  |    ||  ||     |||| || || | ||||     | ||| |  |||| ||||| |||||    | || || |||  |||     ||||||| |||| ||||||||||| || ||||| || || ||||| || |||||||||||||| || |||||| |||||||||| ||| ||||||||||  | |
gtctgcacccgtcaattttcctacgcataacctcatcacaaatatctgacgattttatttaacacaac---tgctaat-tcttcact-----acagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCCATTGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTTTACCAGAAGGCCA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
        | |   |    ||  | |      || ||     |   |  | |||     | | |  |    | ||  | ||   |  |||||| |||| ||||||||||| || ||||| ||||| ||||| || || ||||||||||| |||||||||||||| || || |     ||||||||  | |
------gttagttccttaccttattatgg-ttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 2
----gtaagatgtcgaaacaagtctactcacaaacccatctttc-taatcatttcatttatcacaatgagtactcatgtct-ctacttgta-aacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA----------------------------------------------------------------
    |||   |   |     | |     |  |||   ||    | ||       | | |       ||  ||  |||| || || ||  |  |||||||| |||||||||| ||||| || || || || || ||||| || |||||||||||||| || |||||| |||||||||| ||| | ||||||||  | |                                                                
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagaggctggtttatggggccaaggcagaggctgccatcgccattggatttgatgacttcattgcagATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCAACTTGGAGATCAAGAAAGCTGACGGCAATGGTGCATTGATCGCTGAGCAAGTCTTTGAAAAGAC

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
----gtaagatgtcgaaacaagtctactcacaaacccatctttc-taatcatttcatttatcacaatgagtactcatgtct-ctacttgta-aacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
    |||   |   |     | |     |  |||   ||    | ||       | | |       ||  ||  |||| || || ||  |  |||||||| |||||||||| ||||| || || || || || ||||| || |||||||||||||| || |||||| |||||||||| ||| | ||||||||  | |
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaa-acagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
||  ||| ||  |||     || ||   |    ||  |   |   ||      | | ||    || | || |||       ||||   |||||| |||| ||||||||||| || ||||| || || ||||| || |||||||| ||||| ||||||||| | ||||| || |||   || |||||  | |
gtt-gatttcttaacttacatattcttca---tatgatagaatatatggagcatgttactgatagcaatcttgttcaatgctgtactgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 4
gtaagatgtcgaaacaagt--ctactcacaaacccatctttctaatcat-ttcatt---tatcacaatgagtactcatgtctctacttgta-aacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
       || | ||    |  ||| ||  |     ||||||   | ||| || ||    | |     | | |  | |  |   |  || |  |||||||||||||||||||||| || ||||| ||||| || || || ||||||||||| ||||| || ||||| ||| |||| || ||  | || |||||| | |
-------gttggaatgccttgctattcctatgagtatcttttataccatgtttatcctgttttgagctaacttattacattgttctttttctaacagAGGTTGGTTTATGGAGCGAAGGCCGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCCGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCAA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
-gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
  ||  ||| |     |   |||                  |  | ||    ||| |  | |        |||   |||  || ||| |||||||||||||||||||| || || || ||||| || || || ||||||||||| ||||| || |||||  || |||| || ||  | || |||||| | |
gttagaatggcttgttatccctatgtgtctcttttataccatgtttatcctgtttctagctaacttattacattattctttttctaa-cagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
-----gtaagatgtcgaaacaagt----ctactcacaaacccatctttctaatcatt-tcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
       |  || || ||  || |     |||    |||   |  | | | |  ||  | | || |    | |  | || |      ||  | || ||||||||||||||||||||| || || || ||||| || || || ||||| |||||||||||  | ||||| ||| |||| || ||  | || |||||  |  
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaagatgtcgaaacaagt-ctactcacaa-acccatctt---tctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
             | |||    ||  | || || ||   | ||||| |   |   | || ||   | ||||   | |    || | |  ||  ||     ||||| ||||| ||||| |||||||| |||||||||||||| || || || || || || ||||| ||||| || || || || ||  ||||||| ||  || 
gtctaaataccctacgtctcttcattttcttctaacgttaaccatcgtacattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcagAGATTGGTCTATGGGGCCAAAGCTGAAGCAGCTATAGCTATTGGATTCGACGATTTTATAGCAGATGCCTTAAGGGGTACTGGATTTTACCAAAAGGCTC

upper sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S21_311V6.2 (Physcomitrella patens), 3'ss of exon 5
-------------------------------gtaagatgtcgaaacaagtctactcaca---aacccatctttctaatcatttcattt--------atcacaatgagtactcat-gtctcta------cttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAA-TCTA
                                |    |||  |    ||| ||    ||     |    |||| ||||  | | ||||        ||||   |  |  ||    || | |        || |  |||||| ||||| ||||||||  |||| || |||||  ||||||| || || ||||||||||||||||||||  |  |||| || |     || || ||| ||| 
gtatagtagttgtgctatggctaaaatactaatcctttgttcacctgagtttaacaccatgtggcattcctttgtaatggtcttattttgaagtatatcaagttcggggcttgcagtgtttgaatgactttttgcacagAGATTGGTATATGGAGCACAAGCAGAGGCAGCACTAGCCATTGGCTTCGATGACTTCATAGCTGATGCAATTCGAGGTACAGCCCAGTATCAAAAAGTCT-

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|125285631|gb|EL299716.1|EL299716
EST:     GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAG                         AGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAG
genomic: GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAG
EST: gi|301501150|gb|HO206690.1|HO206690
EST:     GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAG                         AGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
genomic: GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
EST: gi|124731090|gb|EH822492.1|EH822492
EST:     CTCTCGAGACTCAAG                         AGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
genomic: CTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
EST: gi|125182947|gb|EL198124.1|EL198124
EST:     CGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAG                         AGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
genomic: CGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
EST: gi|301502126|gb|HO207666.1|HO207666
EST:     GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAG                         AGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
genomic: GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGAT
EST: gi|124933634|gb|EL010775.1|EL010775
EST:     GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAG                         AGGTTGGTTTATGG
genomic: GTGAGCCATGTCCGATGTGCTTCGGAGCCATCCATCTCTCGAGACTCAAGgtaagatgtc ... ttgtaaacagAGGTTGGTTTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA
  ttctaat  putative branch site (score: 2)
                                      tctctactt  putative PPT
     taatcatttcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG