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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatgggtcattttgattctactaagtttaaactgaaattcacacttttcaacagtactttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTT

Basic information

species Zea mays
transcript GRMZM5G825110_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 3
--------------------------gtaagttatgggtcattttgattctactaagtttaaactgaaattcacacttttcaacagta--ctttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTT
                           | || |  |  |  |||| | |||  ||  |   | |  ||    |  |||||||| ||||  | | || |  |   ||  |||||| |   ||    |||  | ||| ||||||||||||||||| |||||| |||  ||||||||||| ||||||||||| |||||||| || ||||||||||||||||||||  | |||||||| || 
gtaggtcatttcaattgtactatgatttgagctg-gaattttttttaatctcgtagatgccatc--aatgcaatgcttttcaaaagtatgcctattctgttcaagttctttatgtaagggt----tttttttttgcagGCACTTCTTTTTCACAGCAATGTTGTTTACTTATGGGCGTTTTCTTAGTCGACAGCTTGTTAACACAGTAACTTCAGATCACTTATTGTATAAGGTTGTC
















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|211033695|gb|FL002056.1|FL002056
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGC
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGC
EST: gi|71439838|gb|DR820888.1|DR820888
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|71426534|gb|DR807584.1|DR807584
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|76287486|gb|DV027054.1|DV027054
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|149000638|gb|EE037841.2|EE037841
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|71426083|gb|DR807133.1|DR807133
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|93283949|gb|EB676213.1|EB676213
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|76014867|gb|DT942037.1|DT942037
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
EST: gi|78121241|gb|DV539625.1|DV539625
EST:     AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTG                         GCACTTCTTTTTCACGGAAATGCTGTACACTTATGGGCGCTTTCTTAGTCG
genomic: AGAAAATCCAGTGAAGAGAAACAACTTCCTGGGTTCAGGCTACTGAATTGgtaagttatg ... cctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtactttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTT
                                       tcatttcct  CT-rich tract
     tacttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatgggtcattttgattctactaagtttaaactgaaattcacacttttcaacagtactttttttccttgtgtcatttatgcacaagtgtcatttcctattgtagGCACTTCTTTTTCACGGCAATGCTGTACACTTATGGGCGCTTTCTTAGTCGGCAGCTTGTGAATACAGTAACTTCAGATCACTTGCTTTATAAGGTCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA