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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtccgtttcttgaattgattttcatttcctcaaaatgctgtgctccgaatttgaagtttttctgagatttgttgttcatttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG

Basic information

species Zea mays
transcript GRMZM2G057412_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057412_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g33590.2 (Oryza sativa), 3'ss of exon 9
gtgtccgtttcttgaattgattttcatttcctcaaaatgctgtgctc-cgaatttgaagtttttctgagatttgttgttcatttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
||||  ||||  |   |  ||  | || |     || |  ||||||  |  ||||  |  ||| || |  |||||   || ||  ||||||||||||| |||||||||| |||||||| ||||| ||||||||| |||| 
gtgtttgttttatt--tcaatgattatct----gaacttttgtgcttgcacatttataaatttgctaa--tttgtgtatctttggttagTTGAACTATTTGAGGCGGTTCCTTGGGCGAGGATTTCTGAAGCATGCACAA
















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|74240130|gb|DT648044.1|DT648044
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|93281097|gb|EB673361.1|EB673361
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTTTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|149102607|gb|EE287965.2|EE287965
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|33467969|gb|CF245018.1|CF245018
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|76909352|gb|DV163342.1|DV163342
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|211386247|gb|FL227579.1|FL227579
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|74242217|gb|DT650131.1|DT650131
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|60347261|gb|DN214234.1|DN214234
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|89759386|gb|DY688239.1|DY688239
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|86466198|gb|DY232571.1|DY232571
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|60354297|gb|DN221270.1|DN221270
EST:     CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: CAGGCAAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
EST: gi|89249172|gb|DY620958.1|DY620958
EST:     AAGAATGCCATTTTAAGAGTTACATCATGGCGTGAATCAATACAG                         TTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
genomic: AAGAATGGCATTTTAAGAGTTACATCATGGCGTGAATCAATACAGgtgtccgttt ... catttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgctgtgctccgaatttgaagtttttctgagatttgttgttcatttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG
                                           ttcatttctt  CT-rich tract
                aatttgaagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtccgtttcttgaattgattttcatttcctcaaaatgctgtgctccgaatttgaagtttttctgagatttgttgttcatttcttagTTGAACTATATGAGGCGGTTTCTTGGGCGGGGATTCCTGAAGCATTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC