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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC

Basic information

species Zea mays
transcript GRMZM2G065214_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065214_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g56470.1 (Oryza sativa), 3'ss of exon 2
gtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC
||||||| |    |  |||  ||    | ||   |   ||| |  || |  ||      ||| ||      |||  || |||  ||| | ||     ||||||    |||||||||| |||||||| |||||||||||||| || |||||||| || ||||||||||||||| |||| |||                             
gtgagcacc----attgctccaataaatttgatgtttaaaaat--gtctacgatttt-tcatatctgaattgaaa-ttgcatttgccattttg----accatg----aagGCCATCCTCGGATCATCCACCGCGACATCAAATCCGCCAACATCCTCCTCGACAACAACTTCGAAGCAAAG-----------------------------

upper sequence: GRMZM2G065214_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G18470.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgc-gaccatgtcacgtcggaatcttacatccgccgtgtta-tgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC
|| ||  |   |||||  |    ||| ||  |  ||  || |  | |   | |  | ||  | |    |||     ||    |   |  | |   ||  |  |||  || ||||||||| |||||||||||||||||||||||||| || || |||||  | |||  ||||||  | || | |                             
gtaagttt---taaca-ttcaccattctc-attttcttaaccaagttgcataaaacagagaaagctctgtctctgactagtgttatctttttggctgagaaaatg-gtgcagGCCATCCTCGGATCATTCACCGCGACATCAAGTCTGCAAATATTCTCTTGGACTTCAACTTTGATGCTATG-----------------------------
















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|71428627|gb|DR809677.1|DR809677
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148956647|gb|EC902502.2|EC902502
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCAGGAAGAC--TG-                         G-CATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148952040|gb|EC897826.2|EC897826
EST:     CTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGCCCAACATTCTTCTCG
genomic: CTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148995635|gb|EE034843.2|EE034843
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149109740|gb|EE293528.2|EE293528
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149083030|gb|EE172281.2|EE172281
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149088291|gb|EE177386.2|EE177386
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148935707|gb|EC879751.2|EC879751
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|101396001|gb|EB819929.1|EB819929
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149106764|gb|EE188660.2|EE188660
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148979230|gb|EE026592.2|EE026592
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149073459|gb|EE161764.2|EE161764
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|74237975|gb|DT645889.1|DT645889
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148955911|gb|EC901621.2|EC901621
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTGGCCTACCTGCAGGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149110480|gb|EE294148.2|EE294148
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148939327|gb|EC883844.2|EC883844
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|91873912|gb|EB403869.1|EB403869
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148951983|gb|EC897765.2|EC897765
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149088497|gb|EE177606.2|EE177606
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149005317|gb|EE039868.2|EE039868
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|71430899|gb|DR811949.1|DR811949
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|50325030|gb|CO520156.1|CO520156
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|76289986|gb|DV029554.1|DV029554
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|50327066|gb|CO522192.1|CO522192
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148961342|gb|EE012071.2|EE012071
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|91875516|gb|EB405473.1|EB405473
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|101396441|gb|EB820147.1|EB820147
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149082142|gb|EE171322.2|EE171322
EST:     ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--T--                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: ATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGAgtgagcatcc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC
                  atcttac  putative branch site (score: 3)
                 aatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA