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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCACCTAAGAAGCTGTTGGCATCTGATTCACGGCTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccccattctctgcttttatgattatatattggaatttcgaatggcctgtttgcctgccttcagttttgacaccacccccgagtttctgcaaactttcag

Basic information

species Zea mays
transcript GRMZM2G174644_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 9
CGGCACCTAAGAAGCTGTTGGCATCTGATTCACGGCTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccccattctctgcttttatgattatatatt-ggaatttcgaatggcctgtttgcctgcc-ttcagttttgacaccacccccgagtttctgcaaactttcag
|||| || |||||||| |||||||| || || ||  |||||||||||||||||||||||||||||||||||||||| || || ||  |||| ||||||||||| || | | ||| | | ||          | | || ||  |||    ||     | || |  || | || || |     ||   |  | ||  || ||||||||||
CGGCGCCGAAGAAGCTATTGGCATCGGACTCCCGATTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCAAAATCAGGTTCAGAAAAGAGCAGgtaattgctc-attttgtcctaaacctgcgttgttttaggtgtttaatttgaggcatgtggcaaccatccaattatcttgacatttc--atttcgtggaaactttcag
















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|32929324|gb|CF034136.1|CF034136
EST:     ATTCTTCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: ATGC-CCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|213172926|gb|FM184971.1|FM184971
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGGCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|31349767|gb|CD434124.1|CD434124
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32828292|gb|CD967970.1|CD967970
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|4646520|gb|AI491662.2|AI491662
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|211409590|gb|FL109891.1|FL109891
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGGCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|37394152|gb|CF634347.1|CF634347
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32831759|gb|CD971437.1|CD971437
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|148955741|gb|EC901435.2|EC901435
EST:     GGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: GGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|211409591|gb|FL109892.1|FL109892
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAACAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGG
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGG
EST: gi|76011092|gb|DT938262.1|DT938262
EST:     TATGCCCTCGAGAAGGGTGACATGTTTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32830590|gb|CD970268.1|CD970268
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|17931542|gb|BM268502.1|BM268502
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|61236535|gb|DN586285.1|DN586285
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|20513038|gb|BQ280224.1|BQ280224
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32840657|gb|CD980338.1|CD980338
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|37388868|gb|CF631649.1|CF631649
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|213167873|gb|FM190575.1|FM190575
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|78116425|gb|DV534812.1|DV534812
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|83278633|gb|DV942641.1|DV942641
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32840658|gb|CD980339.1|CD980339
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGANCAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|211178953|gb|FL452254.1|FL452254
EST:     TATGCCCTCGAGAAGGGTGACATGTYTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|60343663|gb|DN210636.1|DN210636
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|149084041|gb|EE173436.2|EE173436
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|110946891|gb|EE167048.1|EE167048
EST:     TATGCCCTCGAGAAGGGTGACATGTGTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGGTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|76011658|gb|DT938828.1|DT938828
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|5510846|gb|AI857230.1|AI857230
EST:     GAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: GAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|211409594|gb|FL109895.1|FL109895
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAACAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32830755|gb|CD970433.1|CD970433
EST:     AATGCCCTCGAGAAGGGTGACATGCCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32928518|gb|CF033330.1|CF033330
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32831226|gb|CD970904.1|CD970904
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|50328676|gb|CO523802.1|CO523802
EST:     AAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: AAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|211409595|gb|FL109896.1|FL109896
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTYCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
EST: gi|32834008|gb|CD973686.1|CD973686
EST:     TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAG                         GCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA
genomic: TATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccc ... aaactttcagGCTCGAGGAACAACAGAGAGCTGAGAAACGAACTCGAGAGGCCAAGGGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCACCTAAGAAGCTGTTGGCATCTGATTCACGGCTGAGGCCTGATAGATATGCCCTCGAGAAGGGTGACATGTCTAAGTCCGGGGCAGAGAAGAGCAGgtactttccccattctctgcttttatgattatatattggaatttcgaatggcctgtttgcctgccttcagttttgacaccacccccgagtttctgcaaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG