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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcaagtggtcaaagtacttaattgtaatgatgctagtagctgttggttcttgactcctttcagttgattaggtttatcttgcactcactaaattatgtttactgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 6
gtatgctcaagtggtcaaagtacttaattgtaatgatgctagtagctgttggttcttgactcctttcagttgattaggtttatcttgcactcactaaattatgtttactgtt-ggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAA---GAGCCATTTAAATTCAAGACCGATGAAG
||||||  ||| | | |   |   | ||  || | ||  |  |  || |  ||     |    |      ||  |   |    | || | | || || ||   ||||||||| | |||||||||| |  ||||| |||||||||||  |  | |||||||||||||||||||| |||   ||||||||| |||||||||| |||||||
gtatgccaaagcg-tgatgcttactgatcttact-attttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG
















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|211281609|gb|FL229383.1|FL229383
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211292816|gb|FL187030.1|FL187030
EST:     TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211294948|gb|FL187036.1|FL187036
EST:     TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|5901160|gb|AW042260.1|AW042260
EST:     GGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: GGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|32936507|gb|CF041326.1|CF041326
EST:     GGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: GGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|33094682|gb|CF054676.1|CF054676
EST:     CAAGGAGGGAGAAGGTTATGGGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211292817|gb|FL187031.1|FL187031
EST:     TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211294944|gb|FL187032.1|FL187032
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAATGAGGGTGCTGTTGTTGAAG                         TCAAAATTATTGGAAAGCTTCAGGATGGCACGGTGTTCACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|33094689|gb|CF054683.1|CF054683
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|32934317|gb|CF039129.1|CF039129
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|32935304|gb|CF040116.1|CF040116
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|33091320|gb|CF051314.1|CF051314
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|47962115|gb|CN844824.1|CN844824
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCACCNAGGGTGCTGTTGTTGAAG                         TCCAAATTATCGGAAAGCTTC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTC
EST: gi|211062769|gb|FL037852.1|FL037852
EST:     TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211294949|gb|FL187037.1|FL187037
EST:     TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: TTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
EST: gi|211281607|gb|FL229381.1|FL229381
EST:     CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAG                         TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC
genomic: CAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaa ... ctgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcagttgattaggtttatcttgcactcactaaattatgtttactgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG
                             cactaaa  putative branch site (score: 2)
                              actaaattatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcaagtggtcaaagtacttaattgtaatgatgctagtagctgttggttcttgactcctttcagttgattaggtttatcttgcactcactaaattatgtttactgttggcagTCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA