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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

Basic information

species Zea mays
transcript GRMZM2G053764_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgtt----ttccaattctgcctgaccg--tgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
       | ||   ||  |||   ||  ||    ||  |||| |   |  |    ||     ||   |||   | |||||   |   ||  ||   | ||| ||  || ||         ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |                    
---gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaat-----agGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtc-gcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
      || ||    ||||||   ||  ||   |||   |  |   |  | |  |  | |  | | ||     ||||  | |  ||   ||   |||| || | |   | || | ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||  | || ||    || ||                   
---ttaatcct--ttctctctctctcaattcatcaaagtt-tcaatctttttgttaatggggtctcttccctttctgttcctgattctgggtcctctttgtcttttctcttccgtaggATGATGAGTGATTACAAGGTGGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTTCATGGACCCAATGACAG-------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
----gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
    ||||   |    ||  | | ||  | | ||||| | ||| |      |     ||      ||| | | |||||  || |||      |||  |  |  | |||   ||| |     |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |                    
gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
||||   |    ||  | | ||  | | ||||| | ||| |      |     ||      ||| | | |||||  || |||      |||  |  |  | |||   ||| |     |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |                    
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 1
----gtgaggatgctggacctctcttggtctgttt--tccaattctgcctgaccgtgt-tctgcttgct-tttttttttgatctggccattcttgccggctttcttggtttatcggcgtcg-cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
    ||||   |   |||  | | || || | ||   |   ||   |  |     ||| |    ||| | | ||||||  || |||    | |||  |  |  | ||| | |  | | ||  |||||||||||| || ||||||||||||| | | |||||||| ||||| || ||||| || |||||| | || ||    || |                    
gtctgtgatcttttcggaattgtttttgtattttcgatttcataaagtgttcttttgtataaatttgttgtcttttttccatttggggtgtgttg--gattgacatggatcag-gtcatcatcagGATGATGAGTGATTACAAGGTGGAGACGATCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
----------------gtgaggatgctggacctctcttggtctgttttccaattctgcctg--accgtgttctgcttgctttttt---ttttgatctgg---ccattcttgccggctttcttg------gtttatcggcg--tcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
                 |  |  | |      | | ||    |   || | ||||    |   | | | ||||  |||  | | |   |||   |||||   |  || |||   | | | |||      |||| ||  |   |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |                    
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcct--gaccgtgttctgcttgctttttttt-----------ttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
  |   || |   || |||  || | |  ||| |  ||||   |        ||| |  ||  |||||| |           |   | || |  ||  | | |  |||  || |       || |     |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |                    
--gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
     |    |       ||||  | | || ||   || | | |||   ||   || | ||  |||| |  | ||  | |||| |||     ||  ||| |||   |   | |  ||        ||||||||||| |||||||||||||||||| | || ||||| ||||| || ||||| ||||||||||  || ||    || |                    
-----gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
                       ||  |||||    ||  |  |       || ||  || |||||||   ||| |        ||    |   |  || |||      ||  |||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||  ||||| ||| | || || |  || |                    
-----------------------gtaagtttttttgttgggattt------ttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgtttt------gttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgaggatgctggacc-tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
           |||   | |  || |   |||||   |||    ||   | | | ||     |       ||| |   |   |   || ||   |||  |  |    |     | ||||||||||| ||||||||||| ||||||||||| ||||| |||   |||||||  || || ||  | || |||   || |                    
-----------ggattgtgttgtgattacttttcttgttcgaattggt-gcggtttggggaatcggcaagttgtt---gttgtatctgacga--ttcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
---------------gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
                   | ||       |  |||| | || |        | ||    |||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| |||||||||||||||||||| |||||||||||| | || ||    || || ||| | || ||    || |                    
gtgagtctcgcctcctctcgaatttcaattccttcttcg-ctctccagtggctatgaaaaacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA--------------------

upper sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gtgaggat-gctggacctc---tcttggtctgttttccaat-tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA
|||||  | ||     |||   | |   |   || | |  | ||     ||||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| |||||||||||||||||||| |||||||||||| | || ||    || || ||| | || ||    || |                    
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|76931861|gb|DV172876.1|DV172876
EST:     GCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: GCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|76294184|gb|DV033752.1|DV033752
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|94476395|gb|EB705353.1|EB705353
EST:     TCCCAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|76294043|gb|DV033611.1|DV033611
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|76931862|gb|DV172877.1|DV172877
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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