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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACCATCTTCTGGGTGGGCGAGTGGTTTATAAAGAAAATGCCATTTGTAAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagcttcttttgcatgcatttctttttttataagtttaatttaaatatattttgcagaagaatatttcttatgtaattattctgttgtcag

Basic information

species Zea mays
transcript GRMZM2G149662_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 5'ss of exon 3
TCAACCATCTTCTGGGTGGGCGAGTGGTTTATAAAGAAAATGCCATTTGTAAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagcttcttttgcatgcat-ttctttttttataagtttaat--ttaaatatattttgcagaagaatatttcttatgtaattattctgtt-gtcag
||||||||||| ||||| || || ||||||||||||||||||||||||||  | || ||||| || ||||||||||||||||||||||| ||||||||||||     |  | | |   ||   || ||| |     ||       ||  | |   | |||   || | |||  |  || ||  ||| ||  |||| | |||
TCAACCATCTTTTGGGTTGGAGAATGGTTTATAAAGAAAATGCCATTTGTTCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgt---atacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcag
















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|149096821|gb|EE182610.2|EE182610
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|78081652|gb|DV510064.1|DV510064
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCCTCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|50323915|gb|CO519041.1|CO519041
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|76288284|gb|DV027852.1|DV027852
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|91053026|gb|EB163444.1|EB163444
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|148956825|gb|EC902729.2|EC902729
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|71771810|gb|DR969747.1|DR969747
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|74034904|gb|DT535394.1|DT535394
EST:     AGACATATATATTCAGCATCNAAAGCAAGTCAGCACTGCAATTTCACCAG                         G
genomic: AGACATATATATTCAGCATC-AAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcag-
EST: gi|74034904|gb|DT535394.1|DT535394
EST:     AGACATATATATTCAGCATCNAAAGCAAGTCAGCACTGCAATTTCACCAG                         G
genomic: AGACATATATATTCAGCATC-AAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcag-
EST: gi|5901280|gb|AW042380.1|AW042380
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|88756505|gb|DY540646.1|DY540646
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACCAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|71440103|gb|DR821153.1|DR821153
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|50331144|gb|CO526270.1|CO526270
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|78077279|gb|DV505713.1|DV505713
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|71772305|gb|DR970241.1|DR970241
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|71446982|gb|DR828032.1|DR828032
EST:     AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagc ... ctgttgtcagATCAAAATACGACTGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACCATCTTCTGGGTGGGCGAGTGGTTTATAAAGAAAATGCCATTTGTAAGACATATATATTCAGCATCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggcagcttcttttgcatgcatttctttttttataagtttaatttaaatatattttgcagaagaatatttcttatgtaattattctgttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG