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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatcatgaatataaattttcttgtcaatgaagatatattgaaccaaaaaccaagcctgagtacgtttgttttttcatgatccag

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 5
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa-tcatgaat------ataaattttcttgtcaatga--agatatattgaaccaaaa---------accaagcctgagtacgtttgttttttcatgatccag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| | || || ||        |||| |  || ||  |||  | | ||| ||| || |||         || |  | |   |  ||||  |||| | || |  ||
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgagaaaacatactgagcccaaacacaactacacaagtcttacttgagttttgttttgcttggttaag

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 5
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa-tcatgaat------ataaattttcttgtcaatgaagat--atattgaaccaaaa--------accaagcctgagt-acgtttgttttttcatgatccag
||||||||||||||| ||||| ||||||||||| |||||||| || ||  ||||||||||||||||||||||||| || || ||| ||||||||||||||||||| | || || ||        |||| |  || ||  |||| |   ||| ||  || |||          |||| |||| |   ||||  |||||| || |  ||
GATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTCACAGgtttggactcttggatcactaaccaaatatatttatccttgaaaaaagatactggccccaaacacaagtagacaagtctgacttgagttttgtttttcttggttaag

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 6
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca------tgaatataaattttcttgtcaatga--agatatattgaa---ccaaaaaccaagcctgagtacgtttgttttttcatgatccag--------------------------------
||| ||||| |   ||||||| ||||| ||   ||| ||||| || ||  ||||||| |||||||| |  ||||| ||||||||| | |||||||||||||||||    |      |||  | | |||||||| | | | |   | | | |   |   | | | ||      | | |   | | |||  | || |||                                   
GATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTCACAGgtttgtggtagtttgttgagaaaatattttcttttaagttattggctctctcatattcctatagacttcctgttattgtatat-tttaattattatctttgttgactctaataatattaaaatgttttccag

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 5
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaa----------tcatgaatataaattttct-tgtcaatga--agatata--ttgaaccaaaaaccaagcctgagtacgtttgttttttcatgatccag
||| || || ||  | ||||||||| | || ||||| ||||| || ||  |||| || || |||||||| ||||| ||||| ||||| ||||||||||||||||| |           | ||   |||| |||  | | | |||||   | |||   ||| |   | |        |   | | | |   |||| |  |||   
GATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTCACAGgtttgtagaattttctcccttgggcataattttattattttaatgactggttattgcttgtattgagagttcttttttttttcttcttcctttttaatatcag-

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|76293904|gb|DV033472.1|DV033472
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|76281817|gb|DV021385.1|DV021385
EST:     ACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: ACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|67031739|gb|CO460488.1|CO460488
EST:     TGAAACGAAAAAATTTCAACATTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|32931459|gb|CF036271.1|CF036271
EST:     TGAAACGAAAAAATTTCAACATTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|76016034|gb|DT943204.1|DT943204
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|71758032|gb|DR955969.1|DR955969
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|76010883|gb|DT938053.1|DT938053
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATTT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|148995051|gb|EE034364.2|EE034364
EST:     AAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: AAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|26456742|gb|CA828325.1|CA828325
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|78113480|gb|DV531871.1|DV531871
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|71758174|gb|DR956111.1|DR956111
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|211012560|gb|FL439511.1|FL439511
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|32934477|gb|CF039289.1|CF039289
EST:     TGAAACGAAAAAATTTCAACATTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
EST: gi|60343210|gb|DN210183.1|DN210183
EST:     TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAG                         TTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT
genomic: TGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatca ... catgatccagTTTGTCAGCGATGTAACAAAATACATCAGTGGTTGCATGGCTTCTCTATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGAACTCTTCACACATGTTCCAGTTCTGCGGAACTTTGTCGAGCACCTGAAACGAAAAAATTTCAACGTTTGCGCTGTTTACCTTCTTGATTCACAGgtttgaatcatgaatataaattttcttgtcaatgaagatatattgaaccaaaaaccaagcctgagtacgtttgttttttcatgatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT