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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtccttttcagcgcctcaccataattttgttcgtctcatagatgtccatgagtcaatggtagttgtagtttgctgctgatagcttcagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacag

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042992_T01 (Zea mays), 5'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 20
AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtccttttcagcgcctcaccataattttgttcgtctcataga--tgtccatgagtcaatggtagttgtagtttgctgctgatagcttcagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacag
 ||||| ||     | ||||| ||  | || || ||||| || ||||| ||||| || || || || |||||||| |||||||||||||||||||| ||||||||       ||  |    |   |||    ||  ||  || ||  |  |||  ||||  ||  | |     |   | ||| ||   |  |||   |      | |                                                               
TGAAGATGCTGTGCCTTGCATAGCGCTATCGAAGAATGATTCTTATGTGATGTCCGCCTCGGGAGGAAAAGTCTCTTTGTTCAATATGATGACATTCAAGgtagag-----cttacgaatttagacattggctttctcagctgatgaacttgtttatgaaacagcgatg--catttctggcttctaggaagttcgctttgtttcttt---------------------------------------------------------------

upper sequence: GRMZM2G042992_T01 (Zea mays), 5'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 20
AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtccttttcagcgcctcaccataattttgttcgtctcatagatgtccatgagtcaatggtagttgtagtttgctgctgatagctt---cagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacag
 ||||| ||     | ||||| ||  | || ||||| ||||| ||||| |||||||| || || || ||||| || |||||||| ||||||||||| |||||| | ||||      |||  |||  |  | | | ||    || | | |    || |     ||  |   ||  |||| |  || ||  ||   ||| |   |||| |||| |  ||| ||| |   | |  |||| | || |                            
TGAAGATGCCGTGCCTTGCATAGCGCTCTCTAAAAACGACTCTTATGTGATGTCTGCGTCCGGAGGGAAAGTTTCTTTGTTCAACATGATGACATTCAAGgtaaa-gtcc------gcgaatcatgaggagtctattttattctttg-ttctaataatatggtgagaagcgt--tttgtttttggtaattttgacagttgtcaatttttattc--tga-cgcttttcttcggattt-tgactcag--------------------------
















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|211316880|gb|FL253816.1|FL253816
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|76280738|gb|DV020306.1|DV020306
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|76934579|gb|DV173944.1|DV173944
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|211316878|gb|FL253814.1|FL253814
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|211316882|gb|FL253818.1|FL253818
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|89761150|gb|DY689280.1|DY689280
EST:     CAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: CAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|211014474|gb|FL291774.1|FL291774
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGMAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|211316883|gb|FL253819.1|FL253819
EST:     TCTGCATCTGGTGGGCAA-GTCTCGTTGTTTCA-TATGATGACATTCANG                         GTCATGACTACTTTCATGGCACCTCCAC
genomic: TCTGCATCTGGTGG-CAAAGTCTCGTTGTT-CAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCAC
EST: gi|89764406|gb|DY691228.1|DY691228
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|76929334|gb|DV171965.1|DV171965
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|5499066|gb|AI854933.1|AI854933
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTCAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
EST: gi|89764424|gb|DY691240.1|DY691240
EST:     TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAG                         GTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC
genomic: TGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTC

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: 281

AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 104

AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 97

AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 88

AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtcc ... tctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGAAGCAACCGCCTGCATTGCATTGTCCAAAAATGACTCCTATGTTATGTCTGCATCTGGTGGCAAAGTCTCGTTGTTCAATATGATGACATTTAAGgtagatgtccttttcagcgcctcaccataattttgttcgtctcatagatgtccatgagtcaatggtagttgtagtttgctgctgatagcttcagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG