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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagtattctagtttcaacattaacatatttatgaacttcaaagtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC

Basic information

species Zea mays
transcript GRMZM2G064023_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 5
atctagtattctagtttcaacattaacata-tttatgaacttcaaa-gtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
 | | |  ||  ||||  ||| |      | ||| |||| || ||| ||| | ||    ||        |  |  |   | | |    ||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||| |||| ||||| ||||||||||| |||||||||||||||||||
-ttttgagttagagttgtaacttagttggaatttgtgaaatttaaacgtgtatcactccat-gttttgctgttggatgtaaatctctctcttttctatccagGGTATTCGTTTCAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCAACAGCAATTAAAGGTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTC

upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 6
---atctagtattctagtttcaacattaacatatttatgaacttcaaa-gtgaagcaacgaatcaca-gcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
   |  |||  || ||| ||  |  || ||   ||| |||| || ||| ||| | ||    ||  |  ||  |        | |    || ||||| |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| | ||| || ||||||||||||||||| ||||||||||
ttaagttagatttttagctt--agtttgac---tttgtgaaatttaaacgtgcatcactctatatcttgctgttggatgtaagtctgtacctctttcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTC
















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|4609628|gb|AI600467.1|AI600467
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|32859373|gb|CD999054.1|CD999054
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
                              taataac  putative branch site (score: 1)
                                    ccacttcttttctatc  CT-rich tract
                            actaataa  TA-rich tract