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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag

Basic information

species Zea mays
transcript GRMZM2G303431_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 7
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatatt-ttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag
|| ||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||||||||| ||   | |     |||  |  |||    ||| |  | || ||||    |         |  | || |   ||||||   | |      | |  || |  |  |||                                                                                           
CTCTTTCTACTTCGAGCTGCTGGATTTCTGCTGCCATGCTATATCATGGCTTGGATATTCAGTATTTTGCATCGCCGGCGACAAAGACAGgtacttc---taat----tctgtatggatctcattgattgtcaataaaatcattattgggctattcttatgg---aggaatgaaatgattggtggaccatctgatcctaa-------------------------------------------------------------------------------------------

upper sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 7
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgt--acctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag
|||||  ||||||| |||||||| |||||  | || |||||||||||||| |||  | |||||||| |||| || || ||||||||||| ||    || | ||   |  |||   |      || ||| |  || |      | ||| ||  |   ||  || |  |  || |    | |  |   ||| | |                                                                                                   
CTTTTCTTGCTTCGTGCTGCTGGATTTCTATTACCTTGCTACATCATGGCTTGGGCAATCAGTATTCTGCAGCGTCGGCGACAAAGACAAgtcagtcttaattatagttatcaatattttcagttttgct--tgcatgtgtttggtttcacgtta-cagaattgattctgagtgcagaattgattttag-acag--------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 6
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag
|||||  ||||||| |||||||| |||||  | || ||||| |||||||| |||  | ||||||||||||| ||||| ||||||||||| |||             | | ||        || |||||  |||  ||   ||||||| | |   |    || |   |   | |   || |         | ||||  ||   |    |  |  |||  | || | ||                                                               
CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgta-------------agtttca-------gtcttggttctgactaatttttgttccgactttgc----taattcggtgttggtttgttc---------tgttttgaaatctt----gctttttggctccaactttg---------------------------------------------------------------

upper sequence: GRMZM2G303431_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA07G35750.2 (Glycine max), 5'ss of exon 6
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag
|||||  |||||||||||||||| |||||  | || ||||| |||||||| |||  | ||||||||||||| ||||| ||||||||||| |||             | | ||        || |||||  |||  ||   || |||  | |  ||    || |   |   | |   || |         | ||||  ||  ||    |  || |||  | || | |||                                                              
CTTTTCTTGCTTCGAGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgta-------------agtttca-------gtcttggttctgactaat-tttattctgatttttc----taattcggtgttggtttgttc---------tgttttgaaatcat----gcttcttggctccaactttgt--------------------------------------------------------------

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|14202618|gb|BG836295.1|BG836295
EST:     TGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGARGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: TGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|71761787|gb|DR959724.1|DR959724
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|89252370|gb|DY624156.1|DY624156
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|149074740|gb|EE163170.2|EE163170
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|37374573|gb|CF623659.1|CF623659
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|211322224|gb|FL096771.1|FL096771
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|32858443|gb|CD998124.1|CD998124
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTG
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTG
EST: gi|61118260|gb|DN559221.1|DN559221
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|32919905|gb|CF024717.1|CF024717
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|211322223|gb|FL096770.1|FL096770
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|22546481|gb|BU098792.1|BU098792
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCCCTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|60401280|gb|DN234087.1|DN234087
EST:     ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
EST: gi|24934168|gb|CA452386.1|CA452386
EST:     ACATCATGGCATGGATATTCAGTATTNTGCATCGCCGTCGACANAGACAG                         GAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC
genomic: ACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCC

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: 146

CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCCAGGGGCCGCGCCCTCCAGTTTGCCATCGCTCCAGACTCCCCCGCCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCCAGGGGCCGCGCCCTCCAGTTTGCCATCGCTCCAGACTCCCCCGCCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCCAGGGGCCGCGCCCTCCAGTTTGCCATCGCTCCAGACTCCCCCGCCACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatt ... ttgtctgcagGAAGAGGCTGCACTGGCGGCTGCAGAGGTGGCCTTCATCCTACAGTCGGCCAGGGGCCGCGCCCTCCAGTTTGCCATCGCTCCAGACTCCCCCGCCACCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTTTCTGCTTCGAGCTGCTGGGTTTCTGCTGCCGTGCTACATCATGGCATGGATATTCAGTATTTTGCATCGCCGTCGACAAAGACAGgtacctcatttgacgcaatctcgagagatggtgttggtcatgaaaaaaacttgttccaaatcgtcatcatagtgtaggaataggaagtccaccgtagtatattttttaactatatgtggctcctggtcctaaatctgtcgatgatatggcacaccatccatctaagttctctgtgcttcttcttcttcctttgtctgcag

- - - - - - - - - - - - - - - - - - - - - - - -  CATGGA