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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcgccgcccatggcaaggctgcgcccgcggccgcttccaaagtttctgatttggctcgatcgctcgatcacgcctgacgctccgtggccggacgggattctgcgggttctcgcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATGGGCCTGATCGCGCAGACGGTCCTTGGTGGCGGCTGCAGTGTCCTCGG

Basic information

species Zea mays
transcript GRMZM2G008726_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008726_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g51210.1 (Oryza sativa), 3'ss of exon 1
gtaatgcgccgcccatggcaaggctgcgcccgcg--gccgct-tccaaagtttctgatttggctcgatcgctcgatcacgcctgacgctccgtggccggacgggattctgcgggtt-ctcgcctct---gcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATGGGCCTGATCGCGCAGACGGTCCTTGGTGGCGGCTGCAGTGTCCTCGG
|||||||   ||||   ||   ||   |   | |  |||||  |||    |||  |  ||   | |||   |     |    ||  | ||   |   |       || || |||||  | |  |||   ||||||| |||  |||||||| ||||||||||| ||||| ||||||||| | |||||| |||||||||||||||| |||| |||||||||| |||| |||||
gtaatgctgtgccccgcgcgccgcccggattgggttgccgccctccgggtttttcgggtttttttgattatttcgcta----tggagttcatggtttgatttctgttgtgggggttgtttgattcttgcgcagGTGTCGAGAGGGATCGAGTTGGTCTACGGTGGCGGCAGCGTCGGGTTGATGGGCTTGATCGCGCAGACGGTTCTTGATGGCGGCTGCGGTGTTCTCGG

upper sequence: GRMZM2G008726_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 1
gtaatgcgccgcccatggcaaggctgcgcccgcg--gccgct-tccaaagtttctgatttggctcgatcgctcgatcacgcctgacgctccgtggccggacgggattctgcgggtt-ctcgcctct---gcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATGGGCCTGATCGCGCAGACGGTCCTTGGTGGCGGCTGCAGTGTCCTCGG--
|||||||   ||||   ||   ||   |   | |  |||||  |||    |||  |  ||   | |||   |     |    ||  | ||   |   |       || || |||||  | |  |||   ||||||| |||  |||||||| ||||||||||| ||||| ||||||||| | |||||| |||||||||||||||| |||| |||||||||| |||| |||||  
gtaatgctgtgccccgcgcgccgcccggattgggttgccgccctccgggtttttcgggtttttttgattatttcgcta----tggagttcatggtttgatttctgttgtgggggttgtttgattcttgcgcagGTGTCGAGAGGGATCGAGTTGGTCTACGGTGGCGGCAGCGTCGGGTTGATGGGCTTGATCGCGCAGACGGTTCTTGATGGCGGCTGCGGTGTTCTCGGGT
















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|211040038|gb|FK962663.1|FK962663
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211166478|gb|FK962667.1|FK962667
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211166479|gb|FK962668.1|FK962668
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGGCCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211166480|gb|FK962669.1|FK962669
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211166481|gb|FK962670.1|FK962670
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040035|gb|FK962660.1|FK962660
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACCGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|32823039|gb|CD962748.1|CD962748
EST:     GCAATCGCGCCGTCTACGGGGACGCCGCGCTCGACCTCGGCAAGGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040039|gb|FK962664.1|FK962664
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040036|gb|FK962661.1|FK962661
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040034|gb|FK962659.1|FK962659
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGGCCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040037|gb|FK962662.1|FK962662
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGGCCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|32824305|gb|CD964027.1|CD964027
EST:     GCAATCGCGCCGTCTACGGGGACGCCGCGCTCGACCTCGGCAAGGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211166482|gb|FK962671.1|FK962671
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040041|gb|FK962666.1|FK962666
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040040|gb|FK962665.1|FK962665
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040031|gb|FK962656.1|FK962656
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040032|gb|FK962657.1|FK962657
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
EST: gi|211040033|gb|FK962658.1|FK962658
EST:     GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTG                         GTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG
genomic: GCAATCGCGCCGTCTACGGGGACGCAGCGCTCGACCTCGGCAAAGAGCTGgtaatgcgcc ... gcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacgcctgacgctccgtggccggacgggattctgcgggttctcgcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATGGGCCTGATCGCGCAGACGGTCCTTGGTGGCGGCTGCAGTGTCCTCGG
     gcctgac  putative branch site (score: 3)
                                        ttctcgcctct  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcgccgcccatggcaaggctgcgcccgcggccgcttccaaagtttctgatttggctcgatcgctcgatcacgcctgacgctccgtggccggacgggattctgcgggttctcgcctctgcagGTGGCGAAGGGGATCGATTTGGTCTACGGCGGCGGGAGCGTCGGGCTCATGGGCCTGATCGCGCAGACGGTCCTTGGTGGCGGCTGCAGTGTCCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG