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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtttataataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT2G46280.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 5
-----------gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaa---atacacatatttaaataaccgtgtatcattgtgtttggtataatat---atagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
           |    |  ||   ||   | ||||||| |  |||  ||| |    |||  |    | || |  | ||  |  | ||  |  | || |  |  |||| | |    |||||| |||||||||||||||||||||| ||||| ||||||||||| || || ||  ||||||| ||||||||||||  |||
gtcagttcttcgcacatagtttccatctta-tgttttagtgagaacaatgatcgtgtggttatcttttcaaagttatattttgctgttcaagaatgagagttctatatttttctttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 5
-----------gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaaa--tacacatatttaaataaccgtgtatcattgtgtttggtataatatat----agATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
           |    || ||   ||   | ||||||| |  |||  ||| ||   | |      |   ||   |||  |   ||| || || |  |     |||| | ||     ||||| |||||||||||||||||||||| ||||| ||||||||||| || || ||  ||||||| |||||||||||   |||
gtcagttctttgcacatggtttctatctta-tgttttagtgagaacaatgatagtgtagttttcttttgcaatgttattttttcgtttagcaataagacacttatattttactttcagATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 5
-------gttagtgtttataataagagtgttttact--tggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataa---tatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
        | |||    | ||||  | ||  |||||  |       |  | | ||  || |   |||  ||| |  |   || | |||| |  ||   |        | |||||| |||||||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||||||  |||
gtgatttttcagttcacagaatataaatgccttactctttttgtgttacatcttgctaactttgcatgcttacaatatt-tgaaccattattattaaaacttgctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 5
---------------gttagtgtttataataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggta-----taatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
               |||| |   | ||  |||    |  | |||         |  | ||  || |    ||| ||| | |    || |   || || ||   |     |    | |||||| |||||||||||||||||||||| ||||| |||||||| || || |||||||||||||| ||||||||||||  |||
gtaatttctttttcagttaataaat-tatcaaggcattactccttttgtgttacttccttgctaacttggtatacttaca-atttttgaactgttctgattaaaacttgctctcttttagATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
gttagtgtttataataagagtgttttacttggaaacat-gtaacctg-gaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
|| ||| | | |  |     | | || || |   |  | ||   ||| ||  |||   |   |  | | |   ||  || || | |||   ||   || |||||||| ||||| |||||||| ||||||||||| ||||||||||| || ||||| ||||| || || |||||||| || ||
gtaagtttgtttgct-----tttcttcctagactatgttgtgtactgtgatgatattgaatgtctacttattttgcttccttttttttttcatttgat-tagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
---gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaaatacacatatttaaataaccgtgt-atcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
     |  | ||| |  |     |  | |  || |     |  | |  || || ||  || |||||   |     | | ||  ||||  ||  | | ||   |||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || |||||||| || ||
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgat---tagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 3
gttagtgtttataataagagtgttttacttggaaaca-tgtaacctggaaaatacacatat-ttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
              || |  | |||| | |    | | | ||   ||     |  |    | || |||  |    |||     | |||  | | ||   |||||||| ||||| |||||||| ||||||||||| || |||||||| || ||||| ||||| || || |||||||| || ||
-------------gtaggtttttttttccttcctatactatatgttgagttctgtaatggtattgaatgtctacttatttcgcttttttatttcat---tagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 6
gttagtgtttataataagagtgttttacttggaaacatg-taacctggaaaatacacatatttaaataaccgtgt-atcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
|||  | ||| |  |     |  | |  || |     |  | |  || || ||  || |||||   |     | | ||  ||||  ||  | | ||   |||||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || |||||||| || ||
gttttttttttttttcctt-tactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgat---tagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G36870.2 (Glycine max), 3'ss of exon 3
gttagtgtttataataagagtgttttacttggaaaca-tgtaacctggaaaatacacatat-ttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG----
              || |  | |||| | |    | | | ||   ||     |  |    | || |||  |    |||     | |||  | | ||   |||||||| ||||| |||||||| ||||||||||| || |||||||| || ||||| ||||| || || |||||||| || ||    
-------------gtaggtttttttttccttcctatactatatgttgagttctgtaatggtattgaatgtctacttatttcgcttttttatttcat---tagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTAT

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
---gttagtgtttata-ataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
    |   | | |||| |||   |||| |    ||      |||    || ||| |     |   | ||| |   | |||   ||  |||| |        |||||||| ||||| |||||||| ||||||||||| || |||||||||||||||||||| |||||||| |||||||| |||||
gtaatagatatctatatatatctgtgtgt-gtgtgtgtgtgtgtg-tgtgtaaactgttgttgggttaattaaattatattcctgcatttgat--------tagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gttagtgtttataataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
     |||  |||||  |   |   |  ||  ||||   || | |    |  |    | |  |   | |||   |||  |  |||     || | |    |  ||||| |  | || || ||||| |||||||| ||||| |||||||||||||||||  |||| || ||||| || || |  ||
gctaagttgatgtttgcaggcattcttcttagcttgtttacttctttattccactgcaaaggtcactgaatccgcgttcacgatttc--ctgatgtc---tgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S28_21V6.2 (Physcomitrella patens), 3'ss of exon 1
-gttagtgtttataat--aagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatat-agATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
  |   | ||||  ||  |   | | | | | |   |   || |||    |||     ||||   | | || | |   | |  || |   |  | |  |   ||||| |  |||||||||||||||||||||| || |||||||||||||| |||||| | |  || |||||||| || | |||
aatgcctttttaccatttatccgagatattcatcacagactgcaactcataaag----catagaaagagaatccttatttaccgtctcgtgattgacgtgccagATTTTCGAAGAGGAAATTGGTGGTGTGAAGGGCCATTTTGGACCTATTAATGCTCTAGTTTTTAATCCTGACGGAAGGAG

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|164146661|gb|ES072383.1|ES072383
EST:     TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGTAGGAAATTGGTAGGTGTGAAAGGTCATTTTGGACCTATAA
genomic: TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGT-GGTGTGAAAGGTCATTTTGGACCTATAA
EST: gi|164165647|gb|ES199902.1|ES199902
EST:     GCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCAATTTTGGACCTATAAA
genomic: GCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCA-TTTTGGACCTATAAA
EST: gi|164228800|gb|ES046587.1|ES046587
EST:     TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAAG                         ATTCTGCAAGTAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAA
genomic: TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAA-Ggttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAA
EST: gi|124891541|gb|EH970443.1|EH970443
EST:     CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGAGGAAATTGGTGGTGTG
genomic: CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAGAGGAAATTGGTGGTGTG
EST: gi|164233562|gb|ES104922.1|ES104922
EST:     CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGTAGGAAATTGGTAGGTGTGAAAGGTCATTTTGGACCTATAA
genomic: CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGT-GGTGTGAAAGGTCATTTTGGACCTATAA
EST: gi|124991615|gb|EL063884.1|EL063884
EST:     CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT
genomic: CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT
EST: gi|164148685|gb|EL998518.1|EL998518
EST:     CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGTAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAA
genomic: CTACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAA
EST: gi|164077341|gb|ES009477.1|ES009477
EST:     TACCACTGATCTATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGTAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAA
genomic: TACCACTGATC-ATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAA
EST: gi|124727090|gb|EH818492.1|EH818492
EST:     TGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT
genomic: TGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT
EST: gi|164079553|gb|ES002318.1|ES002318
EST:     TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAAAG                         ATTCTGCAAGTAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAA
genomic: TACCACTGATCATCGTGCTGGAAAGTTTGAAGCTAAGTTTTACGACAA-Ggttagtgttt ... taatatatagATTCTGCAAG-AGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAA
EST: gi|125185979|gb|EL200933.1|EL200933
EST:     CTGGAAAGTTTGAAGCTAAGTTTTACGACAAG                         ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT
genomic: CTGGAAAGTTTGAAGCTAAGTTTTACGACAAGgttagtgttt ... taatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG
                 aaataac  putative branch site (score: 2)
     atacacatatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgtttataataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA