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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactgaaaatcatatcaaatggaaacactataatgtatctcacttgctactgttttgtttactatacacttatattactgtcacttctgttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTG

Basic information

species Zea mays
transcript GRMZM2G013750_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 2
aaactgaaaatcatatcaa---atggaaacacta-taatgtatctcacttgctactgttttgtttact----atacacttatattactgtcacttctgttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTG
        ||||||  |     ||| |  || || || ||   ||   ||   |||   || |  ||       |    |  | |  | | | |  |  |  || ||||| || ||||| |||||||||||||||||||| |||||||| || || |||||||| ||||||||  | ||||||||||| ||  ||||||| || ||||
--------aatcatgcctgtttatgtatgcaatactattgctgctgcattataacttggttatgcacatgtggcatgtctcaactcttctaattctttatttttacagGCTATCACTGCCATGGTTCAGAAAGCAATGGAGTACATTGACTTAACGCCAGACATGGACACACGTATTGAGCTAATCAAGACGTTGAGCAGTGTATCTG
















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|32931087|gb|CF035899.1|CF035899
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13557648|gb|BG549004.1|BG549004
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|32846815|gb|CD986496.1|CD986496
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211157243|gb|FL334276.1|FL334276
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211187929|gb|FL314081.1|FL314081
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGAT
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGAT
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|20803197|gb|BQ294247.1|BQ294247
EST:     AAACGACCTGTATCGGTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGGTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: AAACGACCAG-ATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
EST: gi|32943967|gb|CF048786.1|CF048786
EST:     TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAG                         GCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA
genomic: TAAACGACCAGATCGTTCTCCTCTCCAAGAGGAGAGGCCAGCTTAAGCAGgttcggttct ... ttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctactgttttgtttactatacacttatattactgtcacttctgttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTG
                                       cttctgttc  CT-rich tract
                  tatacacttatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactgaaaatcatatcaaatggaaacactataatgtatctcacttgctactgttttgtttactatacacttatattactgtcacttctgttcgttgcagGCCATTACTGCTATGGTTCAGAAAGCAATGGACTACATTGATTTGACACCAGACATTGACACACGCGTCGAGCTAATCAAAACACTGAGCAGCGTCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG