Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtaataatctagttttgacattaacatatttatgaatttcaaagtgaagcaatgaatcacatcattcatgcgctaataacgacttcttttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC

Basic information

species Zea mays
transcript GRMZM2G063851_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 5
atgtaataatctagttttgacattaacata-tttatgaatttcaaa-gtgaagcaatgaatcacatcattcatgcgctaataacgacttcttttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
 | |     |  |||| | || |      | ||| |||| || ||| ||| | || |  ||    |   |  ||     | | |    ||||||||||||||||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||| |||| || || ||||||||||| |||||||||||||||||||
-ttttgagttagagttgtaacttagttggaatttgtgaaatttaaacgtgtatcactccat-gttttgctgttggatgtaaatctctctcttttctatccagGGTATTCGTTTCAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCAACAGCAATTAAAGGTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTC

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 6
atgtaataatctag-ttttgacattaacata--tttatgaatttcaaa-gtgaagcaatgaatcacat-cattcatgcgctaataacgacttcttttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
      |||  ||| |||| |  |||   |   ||| |||| || ||| ||| | || |  ||  | | |  |     |  | |    || ||||| ||||||||||||||||||||||||| ||||| |||||||| ||||| ||||||||||| ||||||||||| |  || || ||||||||||||||||| ||||||||||
-----ttaagttagatttttagcttagtttgactttgtgaaatttaaacgtgcatcactctatatcttgctgttggatgtaagtctgtacctctttcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTC
















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|51592469|gb|CV071615.1|CV071615
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     TGATCCAGAGGAG                         GGTATTCGTGTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGGC
genomic: TGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGT-TTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCC
EST: gi|32868179|gb|CF007861.1|CF007861
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|78109451|gb|DV527867.1|DV527867
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
EST: gi|74035022|gb|DT535512.1|DT535512
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG                         GGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagcaatgaatcacatcattcatgcgctaataacgacttcttttctatccagGGTATTCGTTTTAGGGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
                              taataac  putative branch site (score: 1)
                                       cttcttttctatcc  putative PPT
                                           ttttctat  TA-rich tract