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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCAGCAGTGCGCCCGCCGCCGCCACCGAGGCCGGCTGGTACGTGCTTGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgtttccttcactctcctagcaattcaacgcgtttcaagttctgagttttctctccgaggtcggccttagggttcggtctgttctgaaaatcaag...

Basic information

species Zea mays
transcript GRMZM2G171660_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171660_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 5'ss of exon 1
GAGACCAGCAGTGCGCCCGCCGCCGCCACCGAGGCCGGCTGGTACGTGCTTGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgtttccttcactctcctagcaattcaacgcgtttcaagttctgagtt--ttctctccgaggtcggccttagggttcggtctg---ttctgaaaatcaag
       |  |  |    |  | || |  |||||  |||||||||||||| || ||||||||||||  |||||| |||||||||||  | ||||| ||||||  |    || | |  || ||| |  |  || |   || |    | |    |  | |     | ||   |||      |||     |    |||  |||     
CGCGTGGGGGGATCCATGGAGGGCGGCGGCGAGGTGGGCTGGTACGTGCTCGGCCCGAACCAGGAGCACGTCGGCCCCTACGCGCTCTCCGAGCTGCGAGgtatcctcctcttcc--tcccctggacacccacccttttccgccctatcgactagtgcgaatgggggcgtgcccccaccttctcgtagaatctctagaaact---
















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|37417377|gb|CF646341.1|CF646341
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATGTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141172|gb|FL018634.1|FL018634
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAN                         C
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcag-
EST: gi|211141172|gb|FL018634.1|FL018634
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAN                         C
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcag-
EST: gi|211141169|gb|FL018631.1|FL018631
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211475992|gb|FL018624.1|FL018624
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141175|gb|FL018637.1|FL018637
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|50335300|gb|CO530426.1|CO530426
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|149070733|gb|EE159146.2|EE159146
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141170|gb|FL018632.1|FL018632
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|91054747|gb|EB165165.1|EB165165
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|76909704|gb|DV163493.1|DV163493
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|148994746|gb|EE034217.2|EE034217
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141171|gb|FL018633.1|FL018633
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|148966210|gb|EE017166.2|EE017166
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141166|gb|FL018628.1|FL018628
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211475990|gb|FL018622.1|FL018622
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211475989|gb|FL018621.1|FL018621
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
EST: gi|211141165|gb|FL018627.1|FL018627
EST:     TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAG                         AACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG
genomic: TGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgttt ... ccctttgcagAACATTTCGCAAACGGTTATTTCAATGAGAGCACAATGCTCTGGGCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACCAGCAGTGCGCCCGCCGCCGCCACCGAGGCCGGCTGGTACGTGCTTGGACCGAACCAGGAGGGCGTCGGACCCTACGCGCTTGCTGAGCTTCGAGgtggctgtttccttcactctcctagcaattcaacgcgtttcaagttctgagttttctctccgaggtcggccttagggttcggtctgttctgaaaatcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT