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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccacgcgtatagcagtagcaacaataacaaatacccgtgtgctgatcgcatatatcattcatgcggtgctttcctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 18
------------gtaactccacgcgtatagcagta-gcaacaataacaaatacccgtg---tgctgatcgcatat-----atcattcatgcg-gtgctttcctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAG--CAAGCACTGAGCCTGCGCCCTCCCAAC-
             ||| |  |||| | || |   |    | ||||  ||||| |  ||   || |||| ||  ||     |   | | | |  ||| ||||   || ||||||||||| ||||||||||||||  ||||||||||||||| ||| ||    |     ||| ||  |||||||   | |||||   ||||  |    |  ||  
gtaactggaattataa-tatacgcatttaacttcatagtataatag-aaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGCTGTTCATAGTTCTAGGAATAAAGCCTAGCAC---GCCTTTGGAAACGGAATG
















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|60337180|gb|DN204153.1|DN204153
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|29130773|gb|CB381477.1|CB381477
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|76286922|gb|DV026490.1|DV026490
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|3157115|gb|AA979737.1|AA979737
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|60344318|gb|DN211291.1|DN211291
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|32849371|gb|CD989052.1|CD989052
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCA
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCA
EST: gi|32845281|gb|CD984962.1|CD984962
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|211141141|gb|FL467349.1|FL467349
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|213179445|gb|FM183428.1|FM183428
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|33097350|gb|CF057310.1|CF057310
EST:     AGAAGAAGGTCCTTGAGTGGGGTGGGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|32856567|gb|CD996248.1|CD996248
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTAGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|37385849|gb|CF630089.1|CF630089
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAGCAG                         GAACTGGCGGAGATTCTGTTCCACTCTTCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|33101201|gb|CF061161.1|CF061161
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTACAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|32846631|gb|CD986312.1|CD986312
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|32844874|gb|CD984555.1|CD984555
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAGCAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|110219847|gb|EC901745.1|EC901745
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTTTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|74244418|gb|DT652332.1|DT652332
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|110213725|gb|EC895622.1|EC895622
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
EST: gi|60347419|gb|DN214392.1|DN214392
EST:     AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG
genomic: AGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCG

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: 668

GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 613

GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 396

GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1090

GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAGgtaactccac ... cctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatacccgtgtgctgatcgcatatatcattcatgcggtgctttcctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC
                                            tcctgat  putative branch site (score: 1090)
                                       tgctttcct  CT-rich tract
                      atatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactccacgcgtatagcagtagcaacaataacaaatacccgtgtgctgatcgcatatatcattcatgcggtgctttcctgatgcagGAACTGGCGGAGATTCTGTTCCACTCTGCTCTATAGATGGCGCCATGTCCGTAGCGGTAGCTCCTGGAATAAGCAAGCACTGAGCCTGCGCCCTCCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG