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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcacttttctgtactataaacactggtctcattagtgaagctttgatcagctgccattgctccttcaaggcatcgttgtgaatattggttctggaacttctgatatactttgtctagtcagcatatcagtgtctatatttattttctgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG

Basic information

species Zea mays
transcript GRMZM5G846548_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 3'ss of exon 6
gtactcacttttctgtactataaacactggtctcattagtgaagctttgatcagctgccattgctccttcaaggcatcgttgtgaatattggttctggaacttctgatatactttgtctagtcagcatatcagt-gtctata-------tttattttctgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG
                             || |||      |  || |    | ||   || |    | | |    |  |||  | |  | |||     |||  ||| |||  |||  | ||||| || | | | |||||||        | ||| | ||| |||||  |    |||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||
-----------------------------gtgtca-----aattctcttgctaactcgaataggcaatgcca--tcttattgccattgatagtttgtttactgatgagataacttgcttggtcagtattttatttgtctatagggtgtactaattctttgtgctttcacttttcccagGGATCTAACCTTGATAGCAATGCTAAAATGTGGCGCCTAGTTGCAGACTTTATGAATGACCTTG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 2
gtactcacttttctgtactataaacactggtctcattagtgaa---gctttgatc--agctgccat-tgctccttcaaggc--atcgttgtgaatattggttctggaacttctgatatactt-tgtctagtcagc---atatcagtgtctatatttattttc-tgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG
         | | | |   ||| | ||  ||  | |||    |     ||||| |  |  ||| |  | ||   || | ||  |  ||  |  |  |||| |  | |  | |||||   ||  | |||| | |     || |   |   ||||||| | ||  | || |  | |      |||||||| |||||||||||| |||| |||||||||||  | ||||||||  |||||||||||||||
------gtctgtgtctctcatacaaacatgttcctttatcttacttattttgaactgaattgcgaagtactagctctatgcggactgtcatatac-ttggattggcatatgctgattctctcctatctaatgattctgatttttttaattatatttttctttatcttgtcccatctgttgcagGGATCAAATCTTGATAGCTATGCAAAAATGTGGCGATTGGTTGCAGATCTTATGAATGACCTTG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G07190.3 (Glycine max), 3'ss of exon 6
gtactcacttttctgtactataaacactggtctcattagtgaagctttgatc-agctgc-cattgctccttcaaggcatcgttgtgaatattggttctggaactt-ctgatatact-ttgtctagtcagcat--atcagtgtctatatttattttctgttctttctttcccac------cagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG
       ||| |||     | | |   |  | |   |  | ||  ||  |   |  ||  || | ||   || | |||   |     ||| | |   ||| |  | ||| |   || || |||| | |   |  |  | | | |  |||   ||||| ||  |  | |||||       |||||||| ||||||||||||||||| |||||||||||  | ||||||||  ||||||||||||| |
--gtctgcttctctcatacaaacatgttcctttatcttattaattttgaactgaaatgtgcaatactagctctatgcagactgtcatatacttggattggcatatgctgtttctctcttatctaatgattttgaaataatttttgaattatatttctctttgtcttgtcccatatgttgcagGGATCAAATCTTGATAGCAATGCAAAAATGTGGCGATTGGTTGCAGATCTTATGAATGACCTAG

upper sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 5
gtactcacttttctgtactataaacactggtctcattagtgaagctttgatcagctgccattgctccttcaaggcatcgttgtgaatattggttctggaacttctgatatactttgtctagtcagcatatcagtgtctatatttattttctgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG
                                                |  |   ||     | | ||||     ||| |  |  | || | ||||    ||||   | |  ||     | | ||  |      ||   |||||| |      | ||   |||    ||||| || || || ||||||||||| ||||||||||| |||||||| ||| ||||||||||  |||
------------------------------------------------gtgcctatgtagcagattcttccca--atcataatacacatcgattct----cttcccttttctttaag--atttagattggttacgttcttatttaatgggaactgttctgttctt--cagGGTTCCAACCTGGATAGCAATGCAAAAATGTGGCGCCTAGTTGCTGACCTTATGAATGATATTG

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|18654521|gb|BM499326.1|BM499326
EST:     TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAG                         GGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
genomic: TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAGgtactcactt ... ttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
EST: gi|18654522|gb|BM499327.1|BM499327
EST:     TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAG                         GGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
genomic: TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAGgtactcactt ... ttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
EST: gi|18649151|gb|BM497970.1|BM497970
EST:     AGGGATA-TGTTCACCTTTTACCAG                         GGATCTAATC-TGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
genomic: AGGGATATTGTTCACCTTTTACCAGgtactcactt ... ttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
EST: gi|88755251|gb|DY539392.1|DY539392
EST:     TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAG                         GGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT
genomic: TGAGGGACTTGACAGGAATGCTTGGAGGGATATTGTTCACCTTTTACCAGgtactcactt ... ttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctagtcagcatatcagtgtctatatttattttctgttctttctttcccaccagGGATCTAATCTTGATAGCAATGCTAAAATGTGGCGTCTAGTTGCAGACTTTATGAATGACCTTG
                    tctatatttattttct  CT-rich tract
                      tatatttattttctgt  TA-rich tract