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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtggggccatcgtttgattaatcgcccctccctcataataatgtgtacgtgtccaatgtgattgccttttattttggccgggaaacaccatgtgatggaatgcgtgtatggtgtgtgccttcaatttgcag

Basic information

species Zea mays
transcript GRMZM2G099980_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099980_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 7
ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtggggccatcgtttgattaatcgcccctccctcataataatgtgtacgtgtccaatgtgattgccttttattttggccgggaaacaccatgtgatggaatgcgtgtatggtgtgtgccttcaatttgcag
||    | |||||||| |||||||| ||| | || ||||| | |||||||||||  || ||||||||||| ||| |||| |||||| | || |||||||||| ||         | ||    |   | ||   || |  |         |  || ||  ||   |     | |  ||   |                                                      
ATGATGCTGATGATATCTCTGAAGAAGTGTTGCGAGCATCAAGTGCTCTAGAAAACGTCCAGCTAGACCGGAAAGCTCGCAATCTGACGACTTCTTGGAGgttggaactattgcctttcttctttgcaccttccctttttgcctggccatttgtttctgatcatagaatatctgtttccag------------------------------------------------------
















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|60349637|gb|DN216610.1|DN216610
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|5895715|gb|AW036961.1|AW036961
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGGTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|5006225|gb|AI712287.1|AI712287
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|60349938|gb|DN216911.1|DN216911
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|71428990|gb|DR810040.1|DR810040
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAGGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|76283944|gb|DV023512.1|DV023512
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAA
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAA
EST: gi|20513022|gb|BQ280208.1|BQ280208
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|26457465|gb|CA829048.1|CA829048
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|78025444|gb|DV493831.1|DV493831
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|78544427|gb|DV621925.1|DV621925
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATTTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|21626078|gb|BQ620999.1|BQ620999
EST:     GAAAGAAATCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACCAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|211383597|gb|FL452880.1|FL452880
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|61118250|gb|DN559211.1|DN559211
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|31612035|gb|CD568657.1|CD568657
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
EST: gi|12970923|gb|BG267226.1|BG267226
EST:     GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAG                         GCATTCAGAGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT
genomic: GAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtgggg ... caatttgcagGCATTCAGGGGATGGCGCCGAGTAACAACAAGGCTTTGGAGCTGGTTGCTT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATCGACTGCTCTAGAAAGTGTTCAGCTAGACCGCAAATCTCGGAATCTGCCAACATCTTGGAGgtaggtggggccatcgtttgattaatcgcccctccctcataataatgtgtacgtgtccaatgtgattgccttttattttggccgggaaacaccatgtgatggaatgcgtgtatggtgtgtgccttcaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG