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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggctcctggctccctcacgttccctcgccgttcctgccctgccttgcctgcctgcctgctttttgggccaccatgagccggccacgagagattaaccgttcctgagcgacgactcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAAGGGGTATGCGCGCGCATCGTCGGCAAGGTGGAGGCGTACCAGCCTCTGT

Basic information

species Zea mays
transcript GRMZM2G443985_T03
intron # 15
splice site 3'
intron type U2

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|78109374|gb|DV527790.1|DV527790
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|50334375|gb|CO529501.1|CO529501
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|211501781|gb|FL158262.1|FL158262
EST:     CCGCTTCCAGCGAGGGGCAGCAAGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|50324042|gb|CO519168.1|CO519168
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|211535403|gb|FL360264.1|FL360264
EST:     CCGCTTCCAGCGAGGGGCAGCAAGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCSAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|37416678|gb|CF645992.1|CF645992
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|211138015|gb|FL213720.1|FL213720
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|76282427|gb|DV021995.1|DV021995
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|211457548|gb|FL334940.1|FL334940
EST:     CCGCTTCCAGCGAGGGGCAGCAAGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|211138016|gb|FL213721.1|FL213721
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCMAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|71439506|gb|DR820556.1|DR820556
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGAAGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|71765602|gb|DR963539.1|DR963539
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|71314972|gb|DR794105.1|DR794105
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTNCA-GCGAATCGCCGCCAAGGA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCT-CAAGCGAATCGCCGCCAAGGA
EST: gi|89757661|gb|DY687168.1|DY687168
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
EST: gi|148992991|gb|EE033699.2|EE033699
EST:     CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAG                         CTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA
genomic: CCGCTTCCAGCGAGGGGCAGCAGGAGCACATCGCCTCTGATGTCACACAGgtcaggctcc ... actcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaccatgagccggccacgagagattaaccgttcctgagcgacgactcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAAGGGGTATGCGCGCGCATCGTCGGCAAGGTGGAGGCGTACCAGCCTCTGT
                       gattaac  putative branch site (score: 2)
                                              ctcctcc  putative PPT
                      agattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggctcctggctccctcacgttccctcgccgttcctgccctgccttgcctgcctgcctgctttttgggccaccatgagccggccacgagagattaaccgttcctgagcgacgactcctccagCTCATCGGATGGACACCTCTGGTCGAGCTCAAGCGAATCGCCGCCAAGGAAGGGGTATGCGCGCGCATCGTCGGCAAGGTGGAGGCGTACCAGCCTCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG