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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtgttgggcctgttggccgtgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT

Basic information

species Zea mays
transcript GRMZM2G089630_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 4
-------tagtgttgggcctgttggccgtgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
       |  |  | |   | ||| || |   || | | ||  ||||  |   ||  |     | | ||| ||| |||| | |||  ||| ||  ||| |||||||||||||||| ||||||||| ||||||||||||||||||||||||||||||| || |||||||||||||| ||||||||||| ||  ||||| |||| ||||
gtttgtctgctaatagaagtcttgtcccttttctacgcactttcatggcaaattttctta---acactattact-tgttttgtttc-tttgct--tctgtgctgcagTATGTTCATCACCTTCAAAGGAAGTACTCGCTTGGCTCATTCAACCTCTTGGGTCATACTGCTCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTT

upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
tagtgttgggcctgttggccg-tgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctcttt---gctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
 |          |||    || |||  |   | ||   |  ||       ||  ||   |||| |||| |||| ||||    ||| |  |||||   ||||||||| ||||| |||||||||  ||||||||||||||||||||||||||| || || |||||||||||||| |||||||||||  ||||| || |||| ||||
-aacagaaattttgtccctcgctgctgttttcactttta--atggtgaggttttggataattagcact-tgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT

upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
tagtgttgggcctgttggccgtgccctcccccctgccatgatatc-cttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
            |    |   ||  |||   |     |  |||||  || || |   |   ||  |||    |   | ||||||     |   || |||||||||| ||  |||||||  | ||||||||||||  |||||||||||| || || ||||| ||||||||||| || ||| | ||  | ||| | || || |
-----------gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaatattggtgtggttt----ttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT

upper sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT4G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
tagtgttgggcctgttggccgtgccctcccccctgccatgatatccttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
                    ||    ||      || | | | | |  |       | ||||  | |    |  |    |||| |||   |||| |||||||||| ||  | || ||  | |||||||||||| |||||||||||||  | || |||||||||||||| ||||| ||| |||| ||  || | ||||| |
--------------------gtaagttctttga-gctacggtttacacaaagattaagattaagatt----tacacaaagttt-ctctcttttgttgcagTATGTACATTATCTACAGCGAAAGTACTCGCTTAGCTCATTCAACCTACTGGGTCATACTGCTCCAGCTCAGGCTGCAACGTTATTGATAGTCGGTCCAT

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|8382969|gb|BE056017.1|BE056017
EST:     GGTTACTAGCTGCAGCAATAGCTGTTTGGAGCACAGCACTACAGCAGCAT                         TATGTTCACCACCTTCAATGGAAGTATTCGCTTGGCTCATTCAATCTCTTA
genomic: GGTTACTAGCTGCAGTAATAGCTGTTTGGAGCACAGCACTACAGCAGCATgtgagtatta ... tttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT
                                   tttactcctctttgct  CT-rich tract
           atattatca  TA-rich tract