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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgttactgttgtctactattactatccacgagatctggtagctttaaattgttgatataattttattgactaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA

Basic information

species Zea mays
transcript GRMZM5G800734_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G800734_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g33810.5 (Oryza sativa), 3'ss of exon 3
gtaagtgttgttactgttgtctactattactatccacgagatctggtagctttaaattgttgatataattttattgactaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA
         ||   |||||| | ||| || | |  |    |    |    || || ||| ||| ||  |||   | ||| | || ||||| |||||||||||||| ||||||||||||||||| ||||| |||    ||||  |||| |||||| ||  |   ||||||    | ||||||||||||
---------gtaggtgttgtatgctagtatt-tagatataactgtggcttttaaatttgctgagatggtttgcctcacttatttcagGTACTGGAATGACCCTGAAGTTCTTCAAAAGATTGGTCAGGCTATGTCAATTAATTTTCCAGGAGATGCTGCTACTTCCACTACATTGTCTGGACCTGAA
















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|211269360|gb|FL417928.1|FL417928
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAAATGACCCTGAGGTTCTTCAAAAGATTGGC-AGGGCAATGGGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAA-TGACCCTGAGGTTCTTCAAAAGATTGGCCAGG-CAATGGGT
EST: gi|32799332|gb|CD951568.1|CD951568
EST:     AAGCCAATTCTTGATGGGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGCGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|211542101|gb|FL388067.1|FL388067
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|21809484|gb|BQ667802.1|BQ667802
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAG
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAG
EST: gi|213175660|gb|FM183110.1|FM183110
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGANNTTCTTCNNN-GATTGGCCAGGCAAT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAAT
EST: gi|60355695|gb|DN222668.1|DN222668
EST:     CTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: CTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|74034821|gb|DT535312.1|DT535312
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|9953126|gb|BE639709.1|BE639709
EST:     AAGCCAATTCTT-NTGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|20507180|gb|BQ279520.1|BQ279520
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|31558362|gb|CD527574.1|CD527574
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGA
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGA
EST: gi|14242838|gb|BG840655.2|BG840655
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGANGTTCTTCAAAAGAT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGAT
EST: gi|20301094|gb|BQ164037.1|BQ164037
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|211035290|gb|FL425632.1|FL425632
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|211082181|gb|FL396892.1|FL396892
EST:     GCCAATTCTTGATGAGATAGAGAAATGGGGGTCCATCTGCCAATGGTGAA                         GTATTGGAAATGACCCCCTGAGGTCTTTTCAAA-GAT-GGCCAGGGCAATG
genomic: GCCAATTCTTGATGAGATAGAGAA-TGGGGGTCCATCTGC-AATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAA-TGACCC--TGAGGT-TCTTCAAAAGATTGGCCAGG-CAATG
EST: gi|32860620|gb|CF000302.1|CF000302
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGC
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGC
EST: gi|60338870|gb|DN205843.1|DN205843
EST:     ATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: ATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|37398879|gb|CF636759.1|CF636759
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|20300887|gb|BQ163830.1|BQ163830
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|211050742|gb|FL374473.1|FL374473
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGC-ANGNCAATGGGTG
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGG-CAATGGGTG
EST: gi|19057756|gb|BM736423.1|BM736423
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|32798849|gb|CD951085.1|CD951085
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGCGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|32796073|gb|CD948309.1|CD948309
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|19058225|gb|BM736892.1|BM736892
EST:     AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
genomic: AAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGT
EST: gi|211206607|gb|FL376335.1|FL376335
EST:     AGCCAATTCTTGATGAGNATAGAGAATGGGGGTCCATCTGCAATGGTGAA                         GTATTGGAATGGACCCTGAGGTTCTTCAAAAGATTGGC-AGGGCAATGGGT
genomic: AGCCAATTCTTGATGAG-ATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATG-ACCCTGAGGTTCTTCAAAAGATTGGCCAGG-CAATGGGT

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: 220

AGGAGCAGCTTGAGGAGAGGATGGCCCGTATCAAGGAAGATCCATCCTTGAAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

AGGAGCAGCTTGAGGAGAGGATGGCCCGTATCAAGGAAGATCCATCCTTGAAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

AGGAGCAGCTTGAGGAGAGGATGGCCCGTATCAAGGAAGATCCATCCTTGAAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 137

AGGAGCAGCTTGAGGAGAGGATGGCCCGTATCAAGGAAGATCCATCCTTGAAGCCAATTCTTGATGAGATAGAGAATGGGGGTCCATCTGCAATGGTGAAgtaagtgttg ... ctaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacgagatctggtagctttaaattgttgatataattttattgactaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA
                                           gactaaa  putative branch site (score: 137)
                  tttaaattgttgatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttgttactgttgtctactattactatccacgagatctggtagctttaaattgttgatataattttattgactaaatttagGTATTGGAATGACCCTGAGGTTCTTCAAAAGATTGGCCAGGCAATGGGTGTTAACCTTCCCGGAGATTCTAGTGTGTCCACTGTGCTCTCTGGACCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT