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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaacaaaaaaacttctatcatcagggtacatatcattgtatggatgttcatattttcttgttttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 3'ss of exon 24
--------gtaaagaacaaaaaaacttctatcatcagggtacatatcattgtatggatgttcatattttcttgttttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT
        || |  ||||||| | |  |||| ||     |     |  ||  || | | || | | |   | |  |||  ||||  | ||| ||||||||||||| ||   |||| |||||| ||| |||||||||||||| ||||||||||||||| |||||||||| ||| |||| ||||| 
gtaaggatgttacaaacaaaagagcacctatgattcta-tctgcctgcttacatagtt-ttaacaatacttggactttatgcagAAACAGTGTGCTTGGTCCTGTGAATGAATGGAAAATTCTAGACTGTATTGATGTTCACAAATTGCTGGAGACAATCTTTGGTGACCAGGATGTGGCAAAC
















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|7227463|gb|AW566104.1|AW566104
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32924622|gb|CF029434.1|CF029434
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32924627|gb|CF029439.1|CF029439
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211039204|gb|FL261425.1|FL261425
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211362665|gb|FL128443.1|FL128443
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32923660|gb|CF028472.1|CF028472
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32944990|gb|CF049809.1|CF049809
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|60345123|gb|DN212096.1|DN212096
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211089342|gb|FL470619.1|FL470619
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCATCAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211039203|gb|FL261424.1|FL261424
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32924181|gb|CF028993.1|CF028993
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCACCAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32924574|gb|CF029386.1|CF029386
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32924629|gb|CF029441.1|CF029441
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211406573|gb|FL434917.1|FL434917
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCACCAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32923887|gb|CF028699.1|CF028699
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32923761|gb|CF028573.1|CF028573
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|60398052|gb|DN230868.1|DN230868
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|60340635|gb|DN207608.1|DN207608
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|15313502|gb|BI478733.1|BI478733
EST:     ATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|31355959|gb|CD440316.1|CD440316
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCCTGTAAAA-CATGGCAAATTCAAGATTGTATTG
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCC-TGTAAAAACATGGCAAATTCAAGATTGTATTG
EST: gi|67014809|gb|CO443558.1|CO443558
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|33093540|gb|CF053534.1|CF053534
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211430406|gb|FL005437.1|FL005437
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|211543406|gb|FL435454.1|FL435454
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|60349287|gb|DN216260.1|DN216260
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32934431|gb|CF039243.1|CF039243
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
EST: gi|32923755|gb|CF028567.1|CF028567
EST:     ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGG                         GCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA
genomic: ATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGA

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: 210

ACCGAGCAGCTGGTGCTGAAATGATGTATCTCTTAGAGCCAAATAAGAAGATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

ACCGAGCAGCTGGTGCTGAAATGATGTATCTCTTAGAGCCAAATAAGAAGATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

ACCGAGCAGCTGGTGCTGAAATGATGTATCTCTTAGAGCCAAATAAGAAGATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

ACCGAGCAGCTGGTGCTGAAATGATGTATCTCTTAGAGCCAAATAAGAAGATGGAGGCAATTAATTTAATTGAAGATTCAACAAATATTACATCATCAGGgtaaagaaca ... tttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcagggtacatatcattgtatggatgttcatattttcttgttttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT
                              ttcatattttcttgtt  CT-rich tract
                                 atattttcttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagaacaaaaaaacttctatcatcagggtacatatcattgtatggatgttcatattttcttgttttttcgcagGCATAGTTTGCTTGGTCCTGTAAAAACATGGCAAATTCAAGATTGTATTGATGTTCATAAATTGCTGGAGACAGTCTTTGGTGATCAGAATGTTGCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA