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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcgtctaaagagacctcttgaagtaaagcagctgctgatatcttttcgcctaatggtgtattatgcttctgttggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTGACGAGGCGCTTGAGCCCGACATCCAAGCCAAAGACGAACTTGTAAGCAA

Basic information

species Zea mays
transcript GRMZM5G806449_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T03 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 3'ss of exon 16
gtatgttcgtctaaagagacctcttgaagtaaagcagctgctgatatcttttcgcctaatggtgtattatgct-tctgttggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTGACGAGGCGCTTGAGCCCGACATCCAAGCCAAAGACGAACTTGTAAGCAA
        ||     || ||  |    | |||| ||| || | ||||| ||| ||      || | | ||  | ||  |||||||| ||||| || || ||||| || |||||||||||||| ||||| ||||| ||| |||| |||||| |||||||  |||||||||||||||| |||||||| ||||
--------gtacgtggacacaac----aataaaccagttgttaatatcatttggcactcgagtttctaatattatccattggctttgcagGTTGGTATTCACCCGTCTGCTGCTGAAGAGTTTGTGACAATGCGGACCTTGACCAGGCGCGTGAGCCCATCATCCAAGCCAAAGACAAACTTGTAGGCAA
















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|19350945|gb|BM895477.1|BM895477
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|76293304|gb|DV032872.1|DV032872
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|19350946|gb|BM895478.1|BM895478
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|37378953|gb|CF626201.1|CF626201
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|211368053|gb|FL471715.1|FL471715
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|47961792|gb|CN844501.1|CN844501
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|58030045|gb|CX725472.1|CX725472
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|33102541|gb|CF062501.1|CF062501
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|37380707|gb|CF627182.1|CF627182
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|14646262|gb|BI180451.1|BI180451
EST:     TCGCTATTGCGGTAAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|37395251|gb|CF634905.1|CF634905
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|71757895|gb|DR955832.1|DR955832
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCCCCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|76012766|gb|DT939936.1|DT939936
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|16916633|gb|BM072928.1|BM072928
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|110942635|gb|EE162792.1|EE162792
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|31405874|gb|CD484606.1|CD484606
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|91056621|gb|EB167039.1|EB167039
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|56382549|gb|CV985218.1|CV985218
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|71310532|gb|DR791561.1|DR791561
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|37381448|gb|CF627611.1|CF627611
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|6095693|gb|AW120360.1|AW120360
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGGCAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|67025835|gb|CO454584.1|CO454584
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|31664369|gb|CD573094.1|CD573094
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|37377035|gb|CF625088.1|CF625088
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|14243079|gb|BG840745.2|BG840745
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|16927664|gb|BM080733.1|BM080733
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|31664100|gb|CD573280.1|CD573280
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|5670916|gb|AI932179.1|AI932179
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|30088227|gb|CB886432.1|CB886432
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|31611972|gb|CD568594.1|CD568594
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCNCCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|148937230|gb|EC881412.2|EC881412
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|71311903|gb|DR792430.1|DR792430
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|45847417|gb|CN071360.1|CN071360
EST:     TCGCTATTGCGGTAAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|149077607|gb|EE166307.2|EE166307
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
EST: gi|6031612|gb|AI668515.2|AI668515
EST:     TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACT                         GTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG
genomic: TCGCTATTGCGGTTAAATGTGGAGCCACCAAAGCAGACTTCGACAGCACTgtatgttcgt ... ggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctgctgatatcttttcgcctaatggtgtattatgcttctgttggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTGACGAGGCGCTTGAGCCCGACATCCAAGCCAAAGACGAACTTGTAAGCAA
                   gcctaat  putative branch site (score: 3)
                                               cttttc  putative PPT
         atatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcgtctaaagagacctcttgaagtaaagcagctgctgatatcttttcgcctaatggtgtattatgcttctgttggcttttcagGTCGGAATCCACCCTTCCGCTGCTGAAGAGTTCGTGACCATGCGCACCGTGACGAGGCGCTTGAGCCCGACATCCAAGCCAAAGACGAACTTGTAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA