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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgatattttgtttacgaaagctgacaatacaatctctcaaatcttgccatcagtcaatagctgttatcttcatgacggaaaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG

Basic information

species Zea mays
transcript GRMZM2G011456_T03
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 3'ss of exon 20
---------gtactgatattttgtttacgaaagctgacaatacaatctctcaaatcttgccatcagtcaatagctgttatcttcatgacggaaaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG
          |    | |  |  |||      |||| |||||     |||  |||  |||| ||| | | || || |||| |   | |          ||||||||||||||||||||||||||||||||||||||||||| ||      | | ||||||||||||||||| ||||| ||||| |   | || |||
gtacactaaatggcaaaacctgatttttatgtgctggcaataactgttcttgaatagtgccttcaat-attatcttttatgtatctca----------tcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTACCGTCGAAGACGCCTATAGAAGTGCACTTTTGGCGATGCTGCGGTGCAACAAAG
















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|20803221|gb|BQ294271.1|BQ294271
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|40336264|gb|CK370334.1|CK370334
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|5005784|gb|AI711846.1|AI711846
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|60345333|gb|DN212306.1|DN212306
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|78117238|gb|DV535625.1|DV535625
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|32944743|gb|CF049562.1|CF049562
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|20337078|gb|BQ172708.1|BQ172708
EST:     CATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: CATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|71300981|gb|DR786519.1|DR786519
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|211483574|gb|FL225319.1|FL225319
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATYTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|21891446|gb|BQ744659.1|BQ744659
EST:     AATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: AATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|31558383|gb|CD527595.1|CD527595
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|37392891|gb|CF633698.1|CF633698
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|18177852|gb|BM379062.1|BM379062
EST:     CACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: CACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|87155574|gb|DY400363.1|DY400363
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|91876144|gb|EB406101.1|EB406101
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTCCACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|31558384|gb|CD527596.1|CD527596
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|33468107|gb|CF245156.1|CF245156
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|37398225|gb|CF636423.1|CF636423
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|26557923|gb|CA830158.1|CA830158
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|71311076|gb|DR791852.1|DR791852
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|91048537|gb|EB158955.1|EB158955
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
EST: gi|211352737|gb|FL476231.1|FL476231
EST:     GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTG                         GTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC
genomic: GTTCATCTTGGAATCGAGCCAAACACCGCTACACCAAACATGTTCAGCTGgtactgatat ... aaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaaatcttgccatcagtcaatagctgttatcttcatgacggaaaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG
                             ttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgatattttgtttacgaaagctgacaatacaatctctcaaatcttgccatcagtcaatagctgttatcttcatgacggaaaactgtcagGTTCCCGATCTTCTTCCCATTGAGAAAGCCCATCTACGTGCCCGAAGGGTCTCCTATAGAAGTGCACTTCTGGCGGTGCTGTGCCCCCACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT