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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G32790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
        ||  || ||   |||| ||    ||   ||  | ||  |  |   |  |   ||||    | |||  || | | ||||||| |||||||| || || || || || || || || ||||| ||||| |||||||||||||||||||| |
-------gtacatttttctggctc-cacacttgctttctgtgataattgtgcataata-atcttgaaatttttctttctga-agGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 2
------gttgaaaatattttcttgaagctc-tcatctatg---aactccatcattgtgcttggt-----tgtgtgtcttact-gtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       |       |   |  | || | | | |  |||    |  |||    ||||  ||| |     |||| ||  || | |  |    | ||   ||||||| ||||||||||| || || ||||||||||| ||||||||||| || |||||||||||||||||||| |
gtacgaatctgtgggacaattgtaaatcccattacatatatttagttccccatttgtttttgttgcaactgtgcgtaatatttggatacactctttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCGCCTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 12
------gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttact-gtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       |       |   |  | |  |  |||  |      |   |  ||||        ||||||  || | |  |    | ||   ||||||| ||||||| ||| || || ||||||||||| ||||||| |||||| |||||||||||||||||||| |
gtacgaatctgtgggacaattgtaatcccatcacattccccatttgtttttgt-tgcaaccgtgtgtaatatttggatacactgtttgaagGTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCAGTTTGCCTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 4
------gttgaaaatattttcttgaagctct---catctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | || |      ||| |||  | | |  ||||    || |       ||||  |  |  ||  | || | |  | ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaaccctctaacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctaaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 3
------------------gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
                  |||| |||   |||  | | |   | |  |    | |  ||  |  | |     ||||  |  |  ||  | || | |    ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaacccttttat-atgtatttagttccccatttgattttgatcc--aactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 3
------gttgaaaatattttcttgaa---gctctcatctatgaactccatcattgtgcttggtt------gtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | ||    ||  ||| |||  | | |  ||||    || | |      |||  |  |  ||| | || | |    ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattttgatccaacggtgcataatcttgtatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G175541_T02 (Zea mays), 3'ss of exon 3
------gttgaaaatattttcttgaa---gctctcatctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | ||    ||  ||| |||  | | |  ||||    || |       | ||  |  |  ||  | || | |    ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattttgatccaactatgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 1
------gttgaaaatattttcttgaagc---tctcatctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | ||||   |  ||| |||  | | |  ||||    || |       ||||  |  |  ||  | || | |  | ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaagcctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctaaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGATG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 2
gttgaaaatatt----ttcttgaagctctcatctatgaactccatca--ttgtgct-tggttgtgtgtcttact-gtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
||  ||| |  |      |||| |  || ||| ||    | ||||    || || |      ||||||  || | |  |  | | ||   ||||||| ||||||| ||| || || ||||||||||| |||||||||||  | |||||||||||||||||||| |
gtacaaatttgtggaacacttgtaaatcccat-tacattccccatttgtttttgttgcaaccgtgtgtaatatttggatacgttgtttgaagGTTGTGGACTGTCACATGTGTGGAGACCCAAACTCAGTCCTTCGGTTCACCTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 4
------gttgaaaatattttcttgaa---gctctcatctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | ||    ||  ||| |||  | | |  ||||    || |       ||||  |  |  ||  | || | |    ||||||| || |||||||| || || |||||||| || |||||| ||||||| |||||||||||||||||||| |
gtacaaatttatgggacagttgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGAGTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 5
-------gttgaaaatattttcttgaagctct---catctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
        || |    |   |  | || |      ||| |||  | | |  ||||    || |       ||||  |  |  ||  | || | |    ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||| ||||||| |
tgtacaaatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 1
gttgaaaatatt----ttcttgaagctctcatctatgaactccatca--ttgtgct-tggttgtgtgtcttact-gtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
||   || |  |      |||| |  || ||| ||    | ||||    || || |      ||||||  || | |  |  | | ||   ||||||| ||||||||||| || || ||||||||||  |||||||||||  | |||||||||||||||||||| |
gtacgaatttgtgggacacttgtaaatcccat-tacattccccatttgtttttgttgcaaccgtgtgtaatatttggatacgctgtttgaagGTTGTGGACTGTCGCATGTGTGGAGACCCAAACTTAGTCCTTCGGTTCACCTTCATAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 5
------gttgaaaatattttcttgaa---gctctcatctatgaactccatcattgtgcttgg------ttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
       || |    |   |  | ||    ||  ||| |||  | | |  ||||    || |       ||||  |  |  ||  | || | |    ||||||| ||||||||||| || || |||||||| || |||||| ||||||| |||||||||||| ||||||| |
gtacagatttatgggacaattgtaaaccctcttacatgtatttagttccccatttgattttgatccaactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCGCTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 5
------------------gttgaaaatattttcttgaagctctcatctatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
                  |||| ||||  | |    | |   | |  |    | |  ||  |  | |  |  ||||  |  |  ||  | || | |    ||||||| |||||||||||  | || |||||||| || |||||| ||||||| ||| |||||||||||||||| |
gtacaaatttatgggacagttgtaaatcctcttac-atgtatttagttccccatttgattttgatcc--gactgtgcataatcttggatatgctctctgaagGTTGTGGACTGTCGCATGCGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCGTAGAGTTCACTGATGAGG

upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gttgaaaatattttcttga--agctctcatctatgaactccatcattgtgcttggt---tgtgtgtcttactgtgtttggtttta----acagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
        |    ||| |  | || |  | |  |    | |  || |  |   |  || | |    || | ||  |  |  |  | | | |     ||||||||| || || ||  | ||||| ||||||||||| || ||||||||||| ||| | ||||||||||| ||||
cgactccttcctgaatttcgtgttaatgaaccattggttttagacccagtacctacgcgttgccgatgggggttatcttacgaattgctgtggattacagGTTGTAGATTGCCGTGTTTGCGGGGACCCAAACTCTGTGCTTCGGTTTGCTTTCGTGGAGTTCACTGACGAAG

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|86051671|gb|DR347426.1|DR347426
EST:     GTCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAG                         GTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCA
genomic: GTCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAGgttgaaaata ... gttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCA
EST: gi|124968785|gb|EL042719.1|EL042719
EST:     ACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAG                         GTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCA
genomic: ACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAGgttgaaaata ... gttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCA
EST: gi|164232158|gb|EL968027.1|EL968027
EST:     GTCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAG                         GTTGTTGACTGTCGCATA
genomic: GTCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAGgttgaaaata ... gttttaacagGTTGTTGACTGTCGCATA
EST: gi|86051683|gb|DR347438.1|DR347438
EST:     -TCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAG                         GTTGTTGACTGTCGCATA
genomic: GTCACTGAAGAGCAGCTTGCTGGTTTGTTTGTGAGCTGTGGACAGgttgaaaata ... gttttaacagGTTGTTGACTGTCGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaactccatcattgtgcttggttgtgtgtcttactgtgtttggttttaacagGTTGTTGACTGTCGCATATGCGGTGACCCAAACTCGGTCCTTCGGTTTGCATTCATAGAGTTCACTGATGAAG
                              gtcttac  putative branch site (score: 3)
                                              ttttaaca  TA-rich tract