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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgacatctacatcaggctctggcctggccaaaggccgtggcgcccgtggcttgacgcacgtttccgtgtttgggtggtttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA

Basic information

species Zea mays
transcript GRMZM2G065214_T02
intron # 2
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 2
lower sequence: LOC_Os03g56470.1 (Oryza sativa), 3'ss of exon 1
gtcagtgacatctacatcaggctctggcctggccaaaggccg-tggcgcccgtggcttgacgcacgtttccg---tgtttgggtggtttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA
|||||| ||   |  ||||  |||| || |  |        | || | |||    || | |||| | |   |     |     |  | |     |||| |||||   ||||||||||   ||| ||||||||||||||||||||||||| || || ||||| ||||||||||| || |||||||    
gtcagtcac---tcgatca--ctctagcttaccacgccattgctgcctccctcacctcgccgcaagatcaagaaacatccaattcttgttggttcagGGAAAGGCTTGCCGGTGATGCCATGGCCGACGAGGCTGCGCATTGCGCTCGGGTCGGCGAAGGGGCTCGCCTACCTACACGAAGACT----
















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:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148995635|gb|EE034843.2|EE034843
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149109740|gb|EE293528.2|EE293528
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149083030|gb|EE172281.2|EE172281
EST:     ACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: ACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149088291|gb|EE177386.2|EE177386
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148935707|gb|EC879751.2|EC879751
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTC
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagG-AAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTC
EST: gi|101396001|gb|EB819929.1|EB819929
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149106764|gb|EE188660.2|EE188660
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148979230|gb|EE026592.2|EE026592
EST:     AGTTCGTCCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGGTGCGCATTGCGCTCG
genomic: AGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     CCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: CCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149073459|gb|EE161764.2|EE161764
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149110480|gb|EE294148.2|EE294148
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148939327|gb|EC883844.2|EC883844
EST:     GCTGGTCTACCAGTTCGTCCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGGGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|91873912|gb|EB403869.1|EB403869
EST:     GCTCGTTTATCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148951983|gb|EC897765.2|EC897765
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149088497|gb|EE177606.2|EE177606
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149005317|gb|EE039868.2|EE039868
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|71430899|gb|DR811949.1|DR811949
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|50325030|gb|CO520156.1|CO520156
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|76289986|gb|DV029554.1|DV029554
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|50327066|gb|CO522192.1|CO522192
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|148961342|gb|EE012071.2|EE012071
EST:     TCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: TCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|91875516|gb|EB405473.1|EB405473
EST:     GCTCGTCTATCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
EST: gi|149082142|gb|EE171322.2|EE171322
EST:     GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACG                         GAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG
genomic: GCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCG

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 1 RNA-Seqlibrary.


Block sizes: 22 (upstream exon), 28 (downstream exon)
Score: 1

CGCCACCTCGTGTCCCTCGTTGGCCACTGCATCGCCGGCGCGCGCCGCGTGCTCGTCTACCAGTTCGTGCCCAACAAGACCCTCGAGTTCCACCTCCACGgtcagtgaca ... ttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtggcgcccgtggcttgacgcacgtttccgtgtttgggtggtttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA
               gcttgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgacatctacatcaggctctggcctggccaaaggccgtggcgcccgtggcttgacgcacgtttccgtgtttgggtggtttgcacgcagGAAAAGGGCAGCCGGTGATGGAGTGGTCGACGAGGCTGCGCATTGCGCTCGGATCAGCCAAGGGCCTCGCCTACCTGCATGAAGACTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA