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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtcatttaatacctagcttcacttgtctgtattttggctggttttcttattggagattcacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAG

Basic information

species Zea mays
transcript GRMZM2G149751_T06
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 9
----gtgagttgtcat-ttaatacctagcttcacttgtctgtattttggctggttttcttattggagattcacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAG
    || |     ||  | ||  | |  |     |   |  | |||| |    | ||  || |    ||||      ||||||||||||||| || ||||||| |||||||||||||||||||| |||||| |||||| | || |||||||||||||||||||||||||| || ||||||
gtgcgtaacagtccacatcaacgcttcaccgttttcccccttttttttgtctatattgctaattacaattcctgctacagGATCTCTGAGGATGAGTACGTCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAG

upper sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 8
gtgagttgtcatttaatacctagcttcacttgtct---gtattttggctggttttcttattggagattcacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAG
||||||     |  |   |   ||||||||||| |    | ||| | ||   || || || | | | |       |||||||||||||||||| ||| ||| |||||||||||||||||||| |||||| |||||| | || |||||||||||||| ||||| ||||| || ||||||
gtgagtaacagtccacatcaacgcttcacttgtttcccttctttcgtctatattactcatagcaaaatactgctacagGATCTCTGAGGAGGAGTACATCAGTGCCATCAAGGAGGAAATCAGCAAGGTTGTTAAGATCCAGGAAGAGCTTGACATCGATGTCCTTGTTCACGGCGAG
















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|5566727|gb|AI881593.1|AI881593
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|211106467|gb|FL269550.1|FL269550
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAWA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|71436763|gb|DR817813.1|DR817813
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|9794625|gb|BE552933.1|BE552933
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|67018424|gb|CO447173.1|CO447173
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|211107368|gb|FL269551.1|FL269551
EST:     CACAAACCGTTGAGCTCAGGAGGGTCCCGCCGTGAGTACAAGGCAAAAA-                         GATCTCTGAGGAGGAATACGTCACTGCCCATCAGGGAG-AAAT
genomic: CACAAACCGTTGAGCTCAGGAGGGTCC-GCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCC-ATCAAGGAGGAAAT
EST: gi|60396167|gb|DN229036.1|DN229036
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|60346583|gb|DN213556.1|DN213556
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|18650007|gb|BM498826.1|BM498826
EST:     CCACAAACCGNTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGG
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33100706|gb|CF060666.1|CF060666
EST:     ACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: ACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33101475|gb|CF061435.1|CF061435
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|6021577|gb|AW066505.1|AW066505
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|211035272|gb|FL424823.1|FL424823
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|29130233|gb|CB380937.1|CB380937
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33101251|gb|CF061211.1|CF061211
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCNNNNNN                         N
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcag-
EST: gi|33101251|gb|CF061211.1|CF061211
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCNNNNNN                         N
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcag-
EST: gi|33100943|gb|CF060903.1|CF060903
EST:     GAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: GAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33101222|gb|CF061182.1|CF061182
EST:     CCACAAACCGCTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCNNNNNN                         NNTCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33102528|gb|CF062488.1|CF062488
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|22473206|gb|BU037686.1|BU037686
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33101156|gb|CF061116.1|CF061116
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|211107369|gb|FL269552.1|FL269552
EST:     CACAAACCGTTGAGCTCAGGAGGGTCCGCGCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CACAAACCGTTGAGCTCAGGAGGGTCCGC-CGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|148941572|gb|EC886508.2|EC886508
EST:     CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: CCACAAACCGTTGAGCTCAGGAGGGTCCGCCGTGAGTACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
EST: gi|33100968|gb|CF060928.1|CF060928
EST:     ACAAGGCAAAAAA                         GATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT
genomic: ACAAGGCAAAAAAgtgagttgtc ... cacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttcacttgtctgtattttggctggttttcttattggagattcacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAG
                            ttttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtcatttaatacctagcttcacttgtctgtattttggctggttttcttattggagattcacatcgcagGATCTCTGAGGAGGAATACGTCACTGCCATCAAGGAGGAAATCAACAAGGTCGTTAAGCTTCAAGAAGAGCTTGACATTGATGTGCTTGTGCATGGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT