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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgatgcctaaaaatatatttttttggacagtttccccttcgctcctgagtgactgactgctaacacacggccacttcgaaaaaacttgtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGTGCACAAGCCCCTACTTTACTACGACAACAACCTGGTCGGCACCATCACC

Basic information

species Zea mays
transcript GRMZM2G038598_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038598_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g51670.2 (Oryza sativa), 3'ss of exon 2
--------tgttgatgcctaaaaatatatttttttggacagtttccccttcgctcctgagtgactgactgctaacacacggccacttcgaaaaaacttgtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGTGCACAAGCCCCTACTTTACTACGACAACAACCTGGTCGGCACCATCACC
           |||||  | ||| |  |   |  | |   || |     ||  |  ||    |  || |    ||  |||| | ||         |||| |  |||||||| ||||||||||| || ||||| ||||| || |||||||| ||||||||||| |||||||| ||||||||||||||||||||  ||||||||||||| 
aagcaatactatgatgaatgaaa-tgaagagtagtagtaggtattattatctgttttggcgaa--gatttgagacggacggacgct---ggtctgcttggc--tgcagGTTTGAGGCTGTCATCCATTTTGCCGGGCTGAAAGCTGTTGGCGAGAGCGTGCAGAAGCCCCTGCTTTACTACGACAACAACCTCATCGGCACCATCACT

upper sequence: GRMZM2G038598_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 2
-----tgttgatgcctaaaaatatatttttttggacagtttccccttcgctcctgagtgactgactgctaacacacggccacttcgaaaaaacttgtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGTGCACAAGCCCCTACTTTACTACGACAACAACCTGGTCGGCACCATCACC
     || |  ||  |   | || |  |  ||      ||          | |   ||   | ||  ||   | |    |         ||| | |     |||||||||| ||||||||||||||||| || || |||||||| || || || |||   |||||  | | |||||||  |||||| ||  |  ||||||| |  
aatgttgctagtgtttgtcattacacctaattttgtgcttaagataatagttcgtggtttatcacacctgtgaaatattcttacaattcaaaatcg-----gcagGTTCGATGCTGTCATTCACTTTGCAGGCCTGAAGGCTGTAGGAGAAAGTGTGTCGAAGCCTTTGCGTTACTACAGCAACAATCTAATAAGCACCATTAAT
















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|71440044|gb|DR821094.1|DR821094
EST:     GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAG                         GTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
genomic: GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAGgtaaccgaca ... gtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
EST: gi|74237590|gb|DT645504.1|DT645504
EST:     GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAG                         GTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
genomic: GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAGgtaaccgaca ... gtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
EST: gi|78085825|gb|DV514218.1|DV514218
EST:     GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAG                         GTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
genomic: GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAGgtaaccgaca ... gtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
EST: gi|211173419|gb|FK976325.1|FK976325
EST:     GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAG                         GTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
genomic: GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAGgtaaccgaca ... gtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
EST: gi|50324852|gb|CO519978.1|CO519978
EST:     GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAG                         GTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT
genomic: GTTGACCTTCGCGACAGGCACGCGTTGGTGGACATCTTCTCGTCGCACAGgtaaccgaca ... gtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgagtgactgactgctaacacacggccacttcgaaaaaacttgtcgatgcagGTTCGAGGCTGTCATTCACTTTGCTGGGCTCAAGGCTGTTGGGGAGAGCGTGCACAAGCCCCTACTTTACTACGACAACAACCTGGTCGGCACCATCACC
               tgctaac  putative branch site (score: 1)
                                    aaaaaactt  TA-rich tract