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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCGCGCGCGCGTGTCCGGGCGAGAAGAGCTGCCAAGGGATGGAGGCGCTGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccggatcccgctctctgacatctgatattcttcgtcccgcgcatctcggttctgtacaaaatgtgcatgatttgggcggtgtttggttgctcaa...

Basic information

species Zea mays
transcript GRMZM2G179459_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179459_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g32460.1 (Oryza sativa), 5'ss of exon 1
GCGCGCGCGCGCGTGTCCGGGCGAGAAGAGCTGCCA-AGGGATGGAGGCGCTGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttc---ctccggatcccgctctctgacatctgatattcttcgtcccgcgcatctcggttctgtacaaaatgtgcatgatttgggcggtgtttggttgctcaa
|| ||  ||  ||  || | | | |||| |  |  | ||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||     || ||||  |  | ||    ||| |   | |       |        ||||   |    |  | |   |||||   || |      |||     
GCACG-ACGTCCGCTTCAGTGAGGGAAGGGGAGGGAGAGGGATGGATGTGCTGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcggatcccagatctggggcccttcagtctcagtgtttgttagggggaaggaatggttaattttgtagcgggtgcgatttctccgtttccgttttgga---
















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|211127070|gb|FL125800.1|FL125800
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149001142|gb|EE038404.2|EE038404
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149088736|gb|EE177860.2|EE177860
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149032717|gb|EE154943.2|EE154943
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|148996112|gb|EE035378.2|EE035378
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|211128000|gb|FL125817.1|FL125817
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|88757167|gb|DY541308.1|DY541308
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149013869|gb|EE043354.2|EE043354
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|93014497|gb|EB640017.1|EB640017
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|211127986|gb|FL125803.1|FL125803
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149085767|gb|EE175287.2|EE175287
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|101389748|gb|EB816808.1|EB816808
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|211127997|gb|FL125814.1|FL125814
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|149086994|gb|EE176539.2|EE176539
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|148983017|gb|EE028919.2|EE028919
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|211127992|gb|FL125809.1|FL125809
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|21843563|gb|BQ704144.1|BQ704144
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAGTTCAGTACTACTGGCTATGAGCGATCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|211127995|gb|FL125812.1|FL125812
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
EST: gi|148951274|gb|EC896976.2|EC896976
EST:     TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAG                         GCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT
genomic: TGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccgg ... tttttttcagGCTGTTATAAAGCAATTCAGTACTACTGGCTATGAGCGGTCAGATTCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCGCGCGCGCGTGTCCGGGCGAGAAGAGCTGCCAAGGGATGGAGGCGCTGAGGAAGCAGGCGAGCAAGTTCAAGGAGCAGGTCGCCAAGCAGCAGCAGgttcctccggatcccgctctctgacatctgatattcttcgtcccgcgcatctcggttctgtacaaaatgtgcatgatttgggcggtgtttggttgctcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG