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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaggtaacattcaaagaaaaggtgttgtatgctctagttctggttacttaaggctgtagattatgacttatggtattctctaccttgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC

Basic information

species Zea mays
transcript GRMZM2G049382_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G01040.1 (Glycine max), 3'ss of exon 2
actaggtaacattcaaagaaaaggtgttgtatgctctagttctggttacttaa-ggctgtagattat---gacttatggtattctctaccttgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC
      | | ||     ||| |  | ||   |   ||   | |||  |    |    | | ||||      |  | |  ||   |  |  |  | |    |||||| |||| || || |||||||||||||| ||||||||| | |  ||||| || |||||||| || ||||| ||||||||||| || || ||| |||| ||
---cacttatatctgt-gaatatttattacttttgctgtatttggagaaaagataattctggattccctaaatattttctaaaatggagttattatgccgacagTTTATGGAGTAGAATATGCATTTGGAGCCCATGACTATCCAACAAGTGGTGTCTTTGAGGTTGAGCCTCGACAGTGTCCTGGCTTTAAGTTTAGGAAGTC

upper sequence: GRMZM2G049382_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G20500.1 (Glycine max), 3'ss of exon 2
actaggta-acattcaaagaaaaggtgttgtatgctctagttctggttact-taaggctgtagattatgact-tatggtattctctaccttgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC
   |  || | ||   || |     |  | | |||| || ||   |  |   |||  ||| |     ||| | | |  ||   |  |  |  | |  | |||||| |||| || || |||||||||||||| ||||||||| | |  ||||| || || ||||| || ||||| ||||||||||| || || ||| |||| ||
--cacttacatatgtgaatatttattact-tttgctgtatttggagaaaagataattctggattccctgaatattttctaaaatggagttgttatgctgacagTTTATGGAGTAGAATATGCATTTGGAGCCCATGACTATCCAACAAGTGGTGTCTTCGAGGTTGAGCCTCGACAGTGTCCTGGCTTTAAGTTTAGGAAGTC

upper sequence: GRMZM2G049382_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0063g02130.t01 (Vitis vinifera), 3'ss of exon 1
actaggtaacattcaaagaaaa-ggtgttgtatgctctagttctggttacttaaggctgtagattatgacttatggtattctctacct-tgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC
    || |   ||  |         | ||     || |  || |  ||  || |  || ||  ||   |   ||  | |  | | | | ||  | || |||||||||||||| |||||||| |||||||| ||||||||  | |  ||||| ||||||||||| ||||| ||||| |||||||| ||||| ||| ||||  |
-gagggcagtttttgattttggcaattttactgtcttttttttttttttttttaatctctatgttggaatagata-tctgatttgcatgtgcatattgacagTTCATGGTGTAGAGTATGCCTTTGGAGCCCATGACTACCCAACAAGTGGTGTTTTTGAGGTTGAACCCCGGCAATGTCCTGGCTTCAAGTTTAGGAAGGC

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|78077755|gb|DV506187.1|DV506187
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|74237928|gb|DT645842.1|DT645842
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|94476136|gb|EB705094.1|EB705094
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTA
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTA
EST: gi|78109677|gb|DV528093.1|DV528093
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|93014379|gb|EB639899.1|EB639899
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|71775361|gb|DR973239.1|DR973239
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|93016747|gb|EB642267.1|EB642267
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|71437491|gb|DR818541.1|DR818541
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|71444264|gb|DR825314.1|DR825314
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|17970113|gb|BM276864.1|BM276864
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|32919043|gb|CF023855.1|CF023855
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|76015982|gb|DT943152.1|DT943152
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|74241229|gb|DT649143.1|DT649143
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|87298772|gb|DY470775.1|DY470775
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|76015122|gb|DT942292.1|DT942292
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|32943700|gb|CF048519.1|CF048519
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTTTTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCAC
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCAC
EST: gi|71437490|gb|DR818540.1|DR818540
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTTATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATATA-TGGA
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGAT-TAGTGGA
EST: gi|149081435|gb|EE170555.2|EE170555
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|101389927|gb|EB816894.1|EB816894
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|22489209|gb|BU049119.1|BU049119
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|32918957|gb|CF023769.1|CF023769
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|78109421|gb|DV527837.1|DV527837
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|149015537|gb|EE045415.2|EE045415
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|76286587|gb|DV026155.1|DV026155
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
EST: gi|50330365|gb|CO525491.1|CO525491
EST:     CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAG                         TTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG
genomic: CGGCTATGTTTACTGGGCTGGTCTAGGGGTATTTCATTCTGGCATTGAAGgtatgatgcc ... ttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttaaggctgtagattatgacttatggtattctctaccttgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC
                              tattctctaccttgtt  CT-rich tract
             tagattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaggtaacattcaaagaaaaggtgttgtatgctctagttctggttacttaaggctgtagattatgacttatggtattctctaccttgtttctttacagTTCATGGTGTTGAGTATGCATTTGGAGCACATGACTATTCGATTAGTGGAGTTTTTGAGGTGGAACCTCGGCAGTGTCCTGGTTTCAAATTTCGGAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA