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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatgcatattttgcttctaccactaactcctttgacatcatcttttactattcaatcctaatatcttcccttttgctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA

Basic information

species Zea mays
transcript GRMZM2G391936_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 13
gtatgaatgca-tattttgcttctacca--ctaactcctttgacatcatcttttacta------ttcaatcctaatatcttccctt-ttgctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA
| ||| | | | ||  |  ||| |||     |  ||   ||  ||  |  |   |  |      || | || || | | |  | || |||  ||||| || || || || ||||||||||||||||||||||||||||| ||   ||| ||||||||||| 
ggatggagggagtacatcacttttacatgtttgtcttggttatcaatagttcaaaaaaatttattttactcatagtgtgtctcattattgtcctctgaagGAACTGCATAATAGACAAGAATGCGAGGATAGGGAAGAATGTAACAATTTCCAACTCTGAG
















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|71757054|gb|DR954991.1|DR954991
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|13236975|gb|BG354989.1|BG354989
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATGCAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|71324302|gb|DR798853.1|DR798853
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|27753904|gb|BM378096.1|BM378096
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|24763417|gb|CA398592.1|CA398592
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|93281647|gb|EB673911.1|EB673911
EST:     CTTGCAGAGGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAAT-CAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAAGAAAGTGGTAATCT
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAA-GAAAGTGGTAATCT
EST: gi|110195335|gb|EC877232.1|EC877232
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|13558450|gb|BG549806.1|BG549806
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|13126504|gb|BG317074.1|BG317074
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACGACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|211470047|gb|FL442813.1|FL442813
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|18178292|gb|BM379502.1|BM379502
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|71323466|gb|DR798382.1|DR798382
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|89763297|gb|DY690558.1|DY690558
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|31363279|gb|CD447636.1|CD447636
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|32850355|gb|CD990036.1|CD990036
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|16377759|gb|BI992107.1|BI992107
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|31348918|gb|CD433275.1|CD433275
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|12967897|gb|BG264844.1|BG264844
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|50335821|gb|CO530947.1|CO530947
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATACACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|16378153|gb|BI992295.1|BI992295
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCC                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCA                         AAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC
genomic: CTTGCAGAAGGAAAAGTTCCTATTGGGATTGGAGAGAATACAACGATTCAgtatgaatgc ... ctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgacatcatcttttactattcaatcctaatatcttcccttttgctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA
                         tcctaat  putative branch site (score: 2)
                               tatcttcccttttgct  CT-rich tract
            ttttactattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatgcatattttgcttctaccactaactcctttgacatcatcttttactattcaatcctaatatcttcccttttgctctctgcagAAAGTGTATCATAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA