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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttaccccctgatgtttggtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg...

Basic information

species Zea mays
transcript GRMZM2G118014_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttacccc-----ctgatgtttg-----gtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg
||||||||||||   |||||| |||||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||| | ||      | |     |   | |         |   |||   ||   |  ||||   ||||     | |||  | |  || |  ||| | | ||          
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggtta--atttggtgggtaagcgct--------

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttaccccctgatgtttggtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg
 ||||||||||||   || || |  ||||| |||||||| ||||||||||| || |||| ||||| ||| || ||||| ||||| ||||||||| | |||||| |||  ||| |  ||   |  |   |    |   ||   |||||  | | ||||   | |    |||     | |  |   |   ||   | |  | 
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGTCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacct--ttttcttccgttttctcactcctcgttcttcgtttagggcttcatttttttatttatttattccctttttctctgtttccg---tttcag-

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttaccccctgatgtttggtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg
 ||||||||||||   || || |  ||||| |||||||| ||||||||||| || |||| ||||| ||| || ||||| ||||| ||||||||| | |||||| |||  ||| |  ||   |  |   |    |   ||   |||||  | | || |     |  |||  | ||      ||  |       |       
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacct--ttttcttccgttttctcactcctcgttcttcgtttagggcttcattatttt--tttgattccctttctctctgtctccgtttcag------

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt----ttaccccctgatgtttggtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg
 ||||||||||||  ||||||||   | || ||||||||||| || || || || |||||| | | |||||||||||| ||||| ||||||||| | ||||||   |  |     || || |      ||| | |||   |||   ||||  ||    | ||    | || | ||   |     |||   |  ||   |     
AAACGGCGACGTCCGGGAGGTGAATAGGAAGTACTACGACCGAGATGTGTGTCGCCTCTTCTTGGTCGGCCTTTGCCCTCACGAGCTCTTCCAGTTGACGgtactgttctgggactatcctccttgccttgatctgttggtttct-ttagcattggagtctgt---ttggttctcgagaaagtgtgggaaagtggggggaaaaa

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|211384991|gb|FL172470.1|FL172470
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|22491280|gb|BU051203.1|BU051203
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGAGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211063251|gb|FL401238.1|FL401238
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|6626437|gb|AW257969.1|AW257969
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|87153157|gb|DY397946.1|DY397946
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211384992|gb|FL172471.1|FL172471
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211384994|gb|FL172473.1|FL172473
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211390250|gb|FL172490.1|FL172490
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|19350716|gb|BM895248.1|BM895248
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211390254|gb|FL172494.1|FL172494
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|19272599|gb|BM888855.1|BM888855
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211390251|gb|FL172491.1|FL172491
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211387625|gb|FL172488.1|FL172488
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|76284913|gb|DV024481.1|DV024481
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211387618|gb|FL172481.1|FL172481
EST:     GCCGGCTCTTCCTCGCCGGTCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGACCTTGTTCTAAGATTCACTCGCTTCAGCTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|19351463|gb|BM895995.1|BM895995
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211387620|gb|FL172483.1|FL172483
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211387614|gb|FL172477.1|FL172477
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211384990|gb|FL172469.1|FL172469
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|211390252|gb|FL172492.1|FL172492
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|22491491|gb|BU051414.1|BU051414
EST:     GCCGGCTCTTACTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|87152221|gb|DY397010.1|DY397010
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|76020071|gb|DT947241.1|DT947241
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
EST: gi|19351812|gb|BM896344.1|BM896344
EST:     GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACG                         AAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA
genomic: GCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAA

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: 49 (upstream exon), 48 (downstream exon)
Score: 78

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 33

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 56

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 40

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTTGGTCCTTGTTCTAAGATTCACTCGCTTCAACTGCGGAAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGGCTCTTCCTCGCCGGCCTTTGCCCCCACGACCTCTTCCAGCTCACGgtatcctcgtttaccccctgatgtttggtttgtgaattttagttaggtttccgttttgggaataggatatcattatctcatggatgaacggaatgttggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA