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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacccgccttctcccccgcgccctcttccaaggttcgagctagggtttctgcgtgtttgctcagatttcattgttttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACCAGCACGCGTTGAACGGGTACGACGATGAGGAGGTCGACGAGGAGGGGCA

Basic information

species Zea mays
transcript GRMZM2G167356_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167356_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g12850.1 (Oryza sativa), 3'ss of exon 1
gtaacccgccttctcccccgcgccctcttccaaggttcgagctagggtttctgcgtgtttgctcagatttcat-tgt-tttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCA-TGGCGGGGTACCCGGAGGACAACCAGCACGCGTTGAACGGGTACGACGATGAGGAGGTCGACGAGGAGGGGCA-
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gtaatccgccgcgcccctctcctcctcctcctccg--cgagctagggtttcgtcacttttgctcagatttcttctgtgcccggttgcagG-GGCATCGGCGTCGGCGGCGGCGGCGGCGGAGGCGAGCTTGCTGTTGTTGTTGTGTGGGATGGCGGGGTACCCGGAGGAGAACCAGCACG-GGATGAACGG
















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|211045050|gb|FL383276.1|FL383276
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|148946214|gb|EC891510.2|EC891510
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|211107234|gb|FL370789.1|FL370789
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|148932748|gb|EE285380.2|EE285380
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|148939672|gb|EC884331.2|EC884331
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|148935082|gb|EC879124.2|EC879124
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|78116552|gb|DV534939.1|DV534939
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|71439287|gb|DR820337.1|DR820337
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|211449696|gb|FL381428.1|FL381428
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|211319685|gb|FL416782.1|FL416782
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCATAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|78108850|gb|DV527267.1|DV527267
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|71427627|gb|DR808677.1|DR808677
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|71432722|gb|DR813772.1|DR813772
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
EST: gi|78076701|gb|DV505135.1|DV505135
EST:     ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAG                         GCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC
genomic: ACGGTTTGCTCAGGATTCGAACCCCACCTTCTGATTGCTCCGAATCCGAGgtaacccgcc ... ttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggttcgagctagggtttctgcgtgtttgctcagatttcattgttttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACCAGCACGCGTTGAACGGGTACGACGATGAGGAGGTCGACGAGGAGGGGCA
                                           ttttgat  putative branch site (score: 4)
                                        ttgtttt  CT-rich tract
                                  atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacccgccttctcccccgcgccctcttccaaggttcgagctagggtttctgcgtgtttgctcagatttcattgttttgatctcagGCGGCGGTTGCGCAGAAGTTTGCGGCATGGCGGGGTACCCGGAGGACAACCAGCACGCGTTGAACGGGTACGACGATGAGGAGGTCGACGAGGAGGGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG