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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttggaattttggttaggttttaccatttcgaaatatgaaattatctatttagttttttgaatatttatctat...

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttgg--aattttggttaggttttaccat-ttcgaaatatgaaattatctatttagttttttgaatatttatctat
||||||||||||   |||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||||| | ||     || |   |       |      || |   | | | ||  |  | ||     | |     |      ||| |||  ||  ||         
CAACGGCGACGTGCGGGAGGTCAGCCGCAAGTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGCCTCTGCCCCCACGACCTCTTCCAGCTCACGgtaccttcccccttctcagtatccagtatccactcatctccatgatgcttctctgtgttttttttttctttgtgggaggttaatttggtgggtaagcgct---

upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttggaattttggttaggttttaccatttcgaaatatgaaattatctatttagttttttgaatatttatctat
 ||||||||||||   || || |  ||||| |||||||| ||||||||||| || |||| ||||| |||||||||||| ||||| ||||| ||| | |||||| |||  ||  |||  |  |       | |   || | |||||  ||    |||  |  |||  | ||  || |||   | |||   | |        
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGTCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttttcttccgttttctcactcctcgttcttcgtttagggcttcatttttttatttattta-ttccctttttctctgtttccgtttcag-----

upper sequence: GRMZM2G069916_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 1
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttggaattttggttagg-ttttaccatttcgaaatatgaaattatctatttagttttttgaatatttatctat
 ||||||||||||   || || |  ||||| |||||||| ||||||||||| ||||||| ||||| |||||||||||| ||||| ||||| ||| | |||||| |||  ||  |||  |  |       | |   || | |||||  || |  ||||       |    || ||| | |     ||| |            
TAACGGCGACGTCCGTGAAGTCAATCGCAAGTACTACGATCGCGACGTCTGTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttttcttccgttttctcactcctcgttcttcgtttagggcttcattatttttttgattccctttctctctgtctccgtttcag-----------

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|211479946|gb|FL425922.1|FL425922
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211423515|gb|FL160031.1|FL160031
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|67033512|gb|CO462261.1|CO462261
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|71330193|gb|DR801854.1|DR801854
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|148973852|gb|EE024993.2|EE024993
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|76292705|gb|DV032273.1|DV032273
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211420922|gb|FL160021.1|FL160021
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|76920400|gb|DV168155.1|DV168155
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|149014011|gb|EE043527.2|EE043527
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|88756297|gb|DY540438.1|DY540438
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|148952947|gb|EE152420.2|EE152420
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|87157671|gb|DY402460.1|DY402460
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211420926|gb|FL160025.1|FL160025
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|9731138|gb|BE509890.1|BE509890
EST:     CCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGCTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: CCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|148932069|gb|EC875423.2|EC875423
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211420930|gb|FL160029.1|FL160029
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGGAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|71312972|gb|DR793008.1|DR793008
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|149000973|gb|EE038213.2|EE038213
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|88756334|gb|DY540475.1|DY540475
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211420928|gb|FL160027.1|FL160027
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCGAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211024315|gb|FL368572.1|FL368572
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|211142603|gb|FL018649.1|FL018649
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA
EST: gi|9952467|gb|BE639050.1|BE639050
EST:     GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACG                         AAAATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAA
genomic: GCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAA

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), 49 (downstream exon)
Score: 285

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 161

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 182

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgt ... gtgattgcagAAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACGGCGACGTCGAGGAGGTGAGCCGCAACTACTACGACCGCGACGTCTGCCGCCTCTTCCTCGCCGGTCTCTGCCCACACGACCTCTTTCAGCTCACGgtatcctcgtttctcccctgacgtttcgttggaattttggttaggttttaccatttcgaaatatgaaattatctatttagttttttgaatatttatctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA