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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

Basic information

species Zea mays
transcript GRMZM2G053764_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
----gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
    ||||   |    ||  | | ||  | | ||||| | ||| |      |     ||      ||| | | |||||  || |||      |||  |  |  | |||   ||| |     |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
||||   |    ||  | | ||  | | ||||| | ||| |      |     ||      ||| | | |||||  || |||      |||  |  |  | |||   ||| |     |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
        | |   ||| |||   ||  ||   |||   |  |   |  | ||||  | |  | | ||  ||||   |   | ||    | |||  ||| |||        || ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||| | || ||    || |
--------gttaatcctttctctctcaattcatcaaagtt-tcaatcttttttctaatggggtctcttcctgattctgg-gtcctctttgtctt--ttgtttt-------ccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
     |    |       ||||  | | || ||   || | | |||   ||   || | ||  |||| |  | ||  | |||| |||     ||  ||| |||   |   | |  ||        ||||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| ||||||||||  || ||    || |
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatgctggacc-tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
           |||   | |  || |   |||||   |||    ||   | | | ||     |       ||| |   |   |   || ||   |||  |  |    |     | ||||||||||| ||||||||||||||||||||||| ||||| |||   |||||||  || || ||  | || |||   || |
-----------ggattgtgttgtgattacttttcttgttcgaattggt-gcggtttggggaatcggcaagttgtt---gttgtatctgacga--ttcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
---------------gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                   | ||       |  |||| | || |        | ||    |||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcg-ctctccagtggctatgaaaaacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gtgaggat-gctggacctc---tcttggtctgttttccaat-tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
|||||  | ||     |||   | |   |   || | |  | ||     ||||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|5895766|gb|AW037012.1|AW037012
EST:     AAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGAGCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: AAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     CCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: CCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     AAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: AAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     GTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: GTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
      ttttgat  putative branch site (score: 4)
     tttttgat  TA-rich tract