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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttccagggctctgttgcgttccttgcctgaactgcttgttttgtagcaactgtttttttcctcatccattgaactattattgtatctgcaatgg...

Basic information

species Zea mays
transcript GRMZM2G108739_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108739_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g57630.2 (Oryza sativa), 5'ss of exon 3
GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttccagggctctgttgcgttccttgcctgaactgcttgttttgtagcaactgtttttttcctcatccattgaactattattgtatctgcaatgg----
|||| ||||| ||  |||| ||| | |||||||| |||||||| |||||||||||||||||| ||||| | |||||  | ||||    |||||    |  || | | | |    |  ||  ||||  | |  ||     |  |||      
GTGTTTTCACCGAATTGATCCAGGAGATGCAAGTAAAAGGTGTTCAGgttagcttccagggc-ctgtttctttcctaccatgaaaaa-ttgttagaaacgaaatctatatcaagtgttc--ttgatatgtccttaggcttttaattattac
















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|71437430|gb|DR818480.1|DR818480
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|37361488|gb|CF602777.1|CF602777
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18649335|gb|BM498154.1|BM498154
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|19058669|gb|BM737336.1|BM737336
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18450451|gb|BM428729.1|BM428729
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|32936153|gb|CF040965.1|CF040965
EST:     GAGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|32937762|gb|CF042581.1|CF042581
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18649482|gb|BM498301.1|BM498301
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18649277|gb|BM498096.1|BM498096
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18450400|gb|BM428678.1|BM428678
EST:     GTGTGTTCCCTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211120940|gb|FL408170.1|FL408170
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211288445|gb|FL410142.1|FL410142
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|5055707|gb|AI734594.1|AI734594
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|31664378|gb|CD573103.1|CD573103
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211490322|gb|FL377881.1|FL377881
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211132915|gb|FL391880.1|FL391880
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211156337|gb|FL380332.1|FL380332
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|30306470|gb|CD001143.1|CD001143
EST:     GGGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211102481|gb|FL395954.1|FL395954
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|93013476|gb|EB638996.1|EB638996
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211392419|gb|FL378726.1|FL378726
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|19822579|gb|BQ048603.1|BQ048603
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|76929348|gb|DV171972.1|DV171972
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18649532|gb|BM498351.1|BM498351
EST:     GTGTGTTCNCTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211488685|gb|FL428190.1|FL428190
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCT
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCT
EST: gi|211045017|gb|FL382448.1|FL382448
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211474315|gb|FL411624.1|FL411624
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18650000|gb|BM498819.1|BM498819
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18450596|gb|BM428874.1|BM428874
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|18649234|gb|BM498053.1|BM498053
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|78092543|gb|DV520917.1|DV520917
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|78084624|gb|DV513017.1|DV513017
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211491468|gb|FL425155.1|FL425155
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|19822485|gb|BQ048509.1|BQ048509
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
EST: gi|211201385|gb|FL369966.1|FL369966
EST:     GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAG                         GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG
genomic: GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG

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: 47 (upstream exon), 47 (downstream exon)
Score: 240

GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 124

GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 109

GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 187

GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttcc ... ctttaaacagGTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGTTCACTGAGCTGATTCAGCAAATGCAAGTGAAAGGTGTACAGgttagcttccagggctctgttgcgttccttgcctgaactgcttgttttgtagcaactgtttttttcctcatccattgaactattattgtatctgcaatgg

- - - - - - AGCTGA
- - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcatcc