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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga

Basic information

species Zea mays
transcript GRMZM2G129034_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129034_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 4
GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga------------------------------------------------------------------------------------------------------
|||| | |||||||||||||| ||| |||||||  | |||||||| |||||||||||||| ||||||||                                                                                                      
GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgttaactgtttctcacatatgtttcagaaatgttgaaaaaaatttaactctaatcttgttgcag
















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|22490837|gb|BU050760.1|BU050760
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|22490837|gb|BU050760.1|BU050760
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|22490837|gb|BU050760.1|BU050760
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|94474168|gb|EB703126.1|EB703126
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|94474168|gb|EB703126.1|EB703126
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|94474168|gb|EB703126.1|EB703126
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24774115|gb|CA409369.1|CA409369
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24774115|gb|CA409369.1|CA409369
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24774115|gb|CA409369.1|CA409369
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773921|gb|CA409175.1|CA409175
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773921|gb|CA409175.1|CA409175
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773921|gb|CA409175.1|CA409175
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773906|gb|CA409160.1|CA409160
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773906|gb|CA409160.1|CA409160
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773906|gb|CA409160.1|CA409160
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773483|gb|CA408737.1|CA408737
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773483|gb|CA408737.1|CA408737
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773483|gb|CA408737.1|CA408737
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773751|gb|CA409005.1|CA409005
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773751|gb|CA409005.1|CA409005
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...
EST: gi|24773751|gb|CA409005.1|CA409005
EST:     ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTT                         G
genomic: ATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga ... ga-ga ... ga-ga ...

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga

- - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA