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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagatcgcattagtttctgactcattgttgcattattgcatgcattatattgttggacgatgatgatatgacgatatgatgtaag

Basic information

species Zea mays
transcript AC148152.3_FGT005
intron # 1
splice site 5'
intron type U2

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|110500605|gb|EE016262.1|EE016262
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|149080136|gb|EE169156.2|EE169156
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37392275|gb|CF633386.1|CF633386
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|149084307|gb|EE173744.2|EE173744
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148992997|gb|EE033706.2|EE033706
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37386720|gb|CF630548.1|CF630548
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148929194|gb|EC874738.2|EC874738
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37390453|gb|CF632456.1|CF632456
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|113702740|gb|EE680244.1|EE680244
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|113702801|gb|EE680305.1|EE680305
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|211339210|gb|FK955075.1|FK955075
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGGCGCG-TCCC
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGG-CGCGGTCC-
EST: gi|211339202|gb|FK955067.1|FK955067
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|113701821|gb|EE679325.1|EE679325
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148941468|gb|EC886393.2|EC886393
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37386062|gb|CF630204.1|CF630204
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37379802|gb|CF626662.1|CF626662
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148996242|gb|EE035519.2|EE035519
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37380979|gb|CF627341.1|CF627341
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCTGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148996243|gb|EE035520.2|EE035520
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|113703950|gb|EE681454.1|EE681454
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37381636|gb|CF627714.1|CF627714
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|14203935|gb|BG837612.1|BG837612
EST:     GGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAAG-TGGCGCGGTCCA
genomic: GGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACG-AAGCTGGCGCGGTCCA
EST: gi|148941469|gb|EC886394.2|EC886394
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37384691|gb|CF629439.1|CF629439
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148992998|gb|EE033707.2|EE033707
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|14203965|gb|BG837642.1|BG837642
EST:     AAGATTGCSCCGGATCCCGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCSG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGSTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|37379556|gb|CF626522.1|CF626522
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|14204210|gb|BG837887.1|BG837887
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|40336201|gb|CK370271.1|CK370271
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|148965454|gb|EE016263.2|EE016263
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|149080138|gb|EE169157.2|EE169157
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|149084308|gb|EE173745.2|EE173745
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
EST: gi|211339203|gb|FK955068.1|FK955068
EST:     AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCG                         GAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT
genomic: AAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 24

TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCATGTTCGAGCTGCTGTCGGAGTCCCTCGGCATGCCCAGCGACCACCTGCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 378

TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCATGTTCGAGCTGCTGTCGGAGTCCCTCGGCATGCCCAGCGACCACCTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCATGTTCGAGCTGCTGTCGGAGTCCCTCGGCATGCCCAGCGACCACCTGCAC


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 28

TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagat ... atgatgtaagGAACGTGATGATGGAATACGGCGAGGAACTGACGAAGCTGGCGCGGTCCATGTTCGAGCTGCTGTCGGAGTCCCTCGGCATGCCCAGCGACCACCTGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGACCTCTTCGAGTCCGCGGCGGCCGACTGGCGCGACACGCTCTACTGCAAGATTGCGCCGGATCCGGCGCCGCGGGAGCTCGTGCCGGAGCCTCTCCGgtgtgtagatcgcattagtttctgactcattgttgcattattgcatgcattatattgttggacgatgatgatatgacgatatgatgtaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT