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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGGTGACCTCTACGGATGGGGTTGGGGTCGATATGGAAACTTAGGTCTTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatctaatttggcccggcctgtcttttttttccagtttagaatcaacagatccaagtatctgaaagtctactaacacctacatcacttgatact...

Basic information

species Zea mays
transcript GRMZM2G003565_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 5'ss of exon 4
AGACGGTGACCTCTACGGATGGGGTTGGGGTCGATATGGAAACTTAGGTCTTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatctaat---ttggcccggcctgtcttttttttccagtttagaatcaacagatccaagtatctgaaagtctactaacacctacatcacttgatact
||| ||||||||||| |||||||| |||||||||||||||||||| || |||||||| || ||||| || ||| | ||||| ||||||||||||||||||||||||  |||||     | ||||  |   ||   |  || ||  ||    |||| |  |  |   ||   ||||     |  || | |  |  |   |||  
AGATGGTGACCTCTATGGATGGGGCTGGGGTCGATATGGAAACTTGGGGCTTGGTGATCGCAATGATCGGTTGGTACCTGAGAAAGTATCTTCTGTGGAGgtaaatattctaacaagcttgcccttcgcatcccctcctttcaaattcct-tcaatat-ttaattcattaaaaaggaatattccatccaatttccagaatat-

upper sequence: GRMZM2G003565_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G00440.1 (Glycine max), 5'ss of exon 6
-----------------------------------------------AGACGGTGACCTCTACGGATGGGGTTGGGGTCGATATGGAAACTTAGGTCTTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTG-TGGAGgtaaattatctaatttggcccggcctgtcttttttttccagtttagaatcaacagatccaagtatctgaaagtctactaacacctacatcacttgatact
                                               ||| ||  |  | || |||||||||||||| |||||||||||||| ||  | ||||||   ||||| |||||||| | ||| |||||  ||  || || |  ||  |  || || ||   |   | |  | | |      ||     ||| |  | |                                            
ATCAAAATGGTTGCTGCCGGTGCTGAACATAGTGTAGCAATCACTGAAGATGGGAATTTGTATGGATGGGGTTGGGGCCGATATGGAAACTTGGGATTGGgtgaca--aatgatcgtttgctccttgagaaagtgactgttgatgtatatatgtcctcgaactta--caaacttaccatctcaggttagaccttaattatgata--------------------------------------------
















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|74242358|gb|DT650272.1|DT650272
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|78083395|gb|DV511788.1|DV511788
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACTGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|71443885|gb|DR824935.1|DR824935
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|94472276|gb|EB701234.1|EB701234
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|50331209|gb|CO526335.1|CO526335
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|76919945|gb|DV167932.1|DV167932
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|211471121|gb|FL255665.1|FL255665
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|71437421|gb|DR818471.1|DR818471
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|211473657|gb|FL255681.1|FL255681
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|29130842|gb|CB381546.1|CB381546
EST:     CGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: CGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|71771589|gb|DR969526.1|DR969526
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT
EST: gi|76283808|gb|DV023376.1|DV023376
EST:     TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAG                         GGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACTGTT
genomic: TTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatc ... ccttctgtagGGTGAGAAGATGGTGCTTGTGGCATGTGGATGGCGCCATACAATTACGGTT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGGTGACCTCTACGGATGGGGTTGGGGTCGATATGGAAACTTAGGTCTTGGTGACCGTAATGACCGTTTGCTTCCTGAAAAAGTATCTTCTGTGGAGgtaaattatctaatttggcccggcctgtcttttttttccagtttagaatcaacagatccaagtatctgaaagtctactaacacctacatcacttgatact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG