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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC

Basic information

species Zea mays
transcript GRMZM2G065214_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065214_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g56470.1 (Oryza sativa), 3'ss of exon 2
gtgagtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC
    ||||||| |    |  |||  ||    | ||   |   ||| |  || |  ||      ||| ||      |||  || |||  ||| | ||     ||||||    |||||||||| |||||||| |||||||||||||| || |||||||| || ||||||||||||||| |||| |||                             
----gtgagcacc----attgctccaataaatttgatgtttaaaaat--gtctacgatttt-tcatatctgaattgaaa-ttgcatttgccattttg----accatg----aagGCCATCCTCGGATCATCCACCGCGACATCAAATCCGCCAACATCCTCCTCGACAACAACTTCGAAGCAAAG-----------------------------

upper sequence: GRMZM2G065214_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G18470.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgc-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|50327066|gb|CO522192.1|CO522192
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148935707|gb|EC879751.2|EC879751
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGT                        
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--Tgtgagtgagc ... atgcatgaa
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGT                        
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--Tgtgagtgagc ... atgcatgaa
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGT                        
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGAC--Tgtgagtgagc ... atgcatgaa
EST: gi|149082142|gb|EE171322.2|EE171322
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|71428627|gb|DR809677.1|DR809677
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|76289986|gb|DV029554.1|DV029554
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148951983|gb|EC897765.2|EC897765
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149106764|gb|EE188660.2|EE188660
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149083030|gb|EE172281.2|EE172281
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|91873912|gb|EB403869.1|EB403869
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148939327|gb|EC883844.2|EC883844
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|101396441|gb|EB820147.1|EB820147
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|71430899|gb|DR811949.1|DR811949
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149110480|gb|EE294148.2|EE294148
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|101396001|gb|EB819929.1|EB819929
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148995635|gb|EE034843.2|EE034843
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148955911|gb|EC901621.2|EC901621
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTGGCCTACCTGCAGGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|50325030|gb|CO520156.1|CO520156
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148961342|gb|EE012071.2|EE012071
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148979230|gb|EE026592.2|EE026592
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149088497|gb|EE177606.2|EE177606
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149088291|gb|EE177386.2|EE177386
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148956647|gb|EC902502.2|EC902502
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCAGGAAGACT                         GGCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149005317|gb|EE039868.2|EE039868
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|148952040|gb|EC897826.2|EC897826
EST:     CTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGCCCAACATTCTTCTCG
genomic: CTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149109740|gb|EE293528.2|EE293528
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|91875516|gb|EB405473.1|EB405473
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|74237975|gb|DT645889.1|DT645889
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
EST: gi|149073459|gb|EE161764.2|EE161764
EST:     GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACT                         GCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG
genomic: GCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 7

GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC


Block sizes: 38 (upstream exon), 18 (downstream exon)
Score: 2

GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 19

GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTgtgagtgagc ... atgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC
                  atcttac  putative branch site (score: 19)
                 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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagcatccgtaacagcttgaaattgtctgtcatcagaaacttggtttgtgacgcgaccatgtcacgtcggaatcttacatccgccgtgttatgtcaccatgcatgaagGCCATCCCCGGATCATTCACCGCGACATCAAGTCGGCCAACATTCTTCTCGACAACAACTTCCAAGCCAAGGTCGCCGACTTCGGGCTGGCCAAGCTGAC

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