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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttccatgtattatttctgcttgctctagggctctcttcaaaaatttacccgttaatggtccatttaatatattgtattgagattttcaacgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATAT

Basic information

species Zea mays
transcript GRMZM2G146472_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146472_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 1
cttccatgtattatttctgcttgctctaggg--ctctcttcaaaaatttacccgttaatggtccatttaatatattgtattgagatttt----caacgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATAT
      | | |||||||||| |  | || |   || |||| ||  | ||   | ||  |||    | ||   | | ||| ||| || |      | | | |  ||||||||||||||||||||||||| ||||||||||| ||||| || ||||| ||  ||||||||||||| |||||| | |||||||||||||||||||||||
-----ctatcttatttctgcataatttatgatcctatcttgaagtaattctacattg-tggcttgtatatattgtcgtactgaaatatcaatgtatcaattcatagGCATGGATAGATACCAAAGGGTGGAGAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATAT
















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|32830032|gb|CD969710.1|CD969710
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|32829230|gb|CD968908.1|CD968908
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|22542105|gb|BU092543.1|BU092543
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|76930615|gb|DV172453.1|DV172453
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|211499004|gb|FL379821.1|FL379821
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|32828756|gb|CD968434.1|CD968434
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGTG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|76918295|gb|DV167234.1|DV167234
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|31356464|gb|CD440821.1|CD440821
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|67031337|gb|CO460086.1|CO460086
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|31354397|gb|CD438754.1|CD438754
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
EST: gi|148939817|gb|EC884519.2|EC884519
EST:     GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCG                         GCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA
genomic: GTTCAAGATTATCCGGTTTAAAGACATCAGAAGAGGCTGCGgtagtgccaa ... cgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacccgttaatggtccatttaatatattgtattgagattttcaacgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATAT
                 atttaat  putative branch site (score: 4)
                                                ctttt  putative PPT
                 atttaatatattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttccatgtattatttctgcttgctctagggctctcttcaaaaatttacccgttaatggtccatttaatatattgtattgagattttcaacgacttttagGCATGGATAGATACCAAAGGGTAGAGAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG