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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

Basic information

species Zea mays
transcript GRMZM2G053764_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G07540.2 (Glycine max), 3'ss of exon 1
-------------gtctgttttccaattctgcc-tgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
              |    |||||| |   |   | |   | || | ||   |   | | |   | || |  ||  | | |  |||  || |       || |     |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |
gttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 1
----------gtctgttttccaattctgcctgaccgtgttctgcttgct-------tttttttttgatctggccattcttgccggctttcttggtttatcggcgtc-gcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA-
           ||| | |  ||||||  |          |||  ||| |       | | ||     ||||  | |  ||   ||   |||| || | |   | || | ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||  | || ||    || | 
ttaatcctttctctctctctcaattcatcaaagtttcaatctttttgttaatggggtctcttccctttctgttcctgattctgggtcctctttgtcttttctcttccgtaggATGATGAGTGATTACAAGGTGGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTTCATGGACCCAATGACAG

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
--------------------gtctgttttccaattctgcct---gaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                     | | ||||  | ||  |  |   ||  |||||||  |||| |   || |||  | |  |||||   |  | | |   |||   |  ||| |     |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
----------------gtctgttttccaattctgcct---gaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                 | | ||||  | ||  |  |   ||  |||||||  |||| |   || |||  | |  |||||   |  | | |   |||   |  ||| |     |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 1
-----------------------gtctgt-tttccaattctgcctgaccgtgttctgc------ttgct-tttttttttgatctggccattcttgccggctttcttggtttatcggcgtcg-cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                        | ||| ||| | |||           | || ||       ||| | | ||||||  || |||    | |||  |  |  | ||| | |  | | ||  |||||||||||| || ||||||||||||| | | |||||||| ||||| || ||||| || |||||| | || ||    || |
gtctgtgatcttttcggaattgtttttgtattttcgatttcataaagtgttcttttgtataaatttgttgtcttttttccatttggggtgtgttg--gattgacatggatcag-gtcatcatcagGATGATGAGTGATTACAAGGTGGAGACGATCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
----------------------------------------gtctgttttccaattctgcc-tgaccgtgttctgcttgctttttt---ttttgatctgg---ccattcttgccggctttcttg------gtttatcggcg--tcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                                         | |  |||||| |   |   | | | | ||||  |||  | | |   |||   |||||   |  || |||   | | | |||      |||| ||  |   |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G07540.1 (Glycine max), 3'ss of exon 1
---------------------------------gtctgttttccaattctgcc-tgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggt-------ttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                                  |    |||||| |   |   | |   | || | ||   |   | | |   | || |  ||  | | |  |||  || |       || |     |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |
gttaatccaccacttcttctgttttccttttcccttctatttccattaaagttataattttttttttctaattgggtgtctaagtttgactcttgattctgattttgatgttagtttttttttttaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCATTTCCATGGACCCAATGAGA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------gtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                   | | || ||   || | | |||   ||   || | ||  |||| |  | ||  | |||| |||     ||  ||| |||   |   | |  ||        ||||||||||| |||||||||||||||||| | || ||||| ||||| || ||||| ||||||||||  || ||    || |
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
||  |||||    ||  |  |       || ||  || |||||||   ||| |        ||    |   |  || |||      ||  |||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||  ||||| ||| | || || |  || |
gtaagtttttttgttgggattt------ttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgtttt------gttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggcca--ttcttgccggctttcttggtttatcggcgtc-------gcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
 |  ||| ||   |||     |   | |||||   ||| |    |||  |   | | ||  || |||  |  | |   | || |     ||        | ||||||||||| ||||||||||| ||||||||||| ||||| |||   |||||||  || || ||  | || |||   || |
ggattgtgttgtgattactttt---cttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------gtctgttttccaat---tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                                   |  | | |||| |   | ||    |||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| |||||||||||||||||||| |||||||||||| | || ||    || || ||| | || ||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------gtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                             ||  | |||    ||     ||||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| |||||||||||||||||||| |||||||||||| | || ||    || || ||| | || ||    || |
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|47961920|gb|CN844629.1|CN844629
EST:     GCGCCGCGAGATGGACCTTATGAAGCTGTGAGGATGCTGGACCTCTCTTG                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: GCGCCGCGAGATGGACCTTATGAAGCTGTGAGGATGCTGGACCTCTCTTGgtctgttttc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|60355507|gb|DN222480.1|DN222480
EST:     GCGCCGCGAGATGGACCTTATGAAGCTGTGAGGATGCTGGACCTCTCTTG                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: GCGCCGCGAGATGGACCTTATGAAGCTGTGAGGATGCTGGACCTCTCTTGgtctgttttc ... ggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

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