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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctattttttttctggaataggtgaccagctatgctctcaaaaagacagaaccagtgttggcgggtcccacatgagtgggatctgaaaaaggaata...

Basic information

species Zea mays
transcript GRMZM2G038588_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038588_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g12570.1 (Oryza sativa), 5'ss of exon 7
AAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctattttttttctgg-aataggtgaccagctatgctctcaaaaagacagaaccagtgttggcgggtcccacat-gagtgggatctgaaaaaggaata
||  ||| |||||||||||||||||||||||||||||||||| |||||||| |  |||||| |||| || || ||||  || ||||||||||| ||||||||||  ||||||| |  |   || | |||        |    ||||      | |  || ||||           ||| |  ||| |    | |   |||  
AAATAAGCCCAACATTGATGTTGTAAAACTTCATAAATCAGAAGGTGTTGTTCCGAGAAATCCAAAGTACCGTCAAAAGACTAGAAGCTTCCGTATCAAGgtaaattatttttctgataataaaatgtggaagttcctagattcaactttcaaaagtcaatgtttcaatacaaggcattgtttggtaggcaatatgagaa--
















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|71323423|gb|DR798362.1|DR798362
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|148999969|gb|EE037044.2|EE037044
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|149010086|gb|EE041893.2|EE041893
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|50338769|gb|CO533895.1|CO533895
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|31405753|gb|CD484485.1|CD484485
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|50338323|gb|CO533449.1|CO533449
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|71763129|gb|DR961066.1|DR961066
EST:     TCTTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|71324526|gb|DR798964.1|DR798964
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|86471476|gb|DY237846.1|DY237846
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|93014406|gb|EB639926.1|EB639926
EST:     TCTTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|110518920|gb|EE023507.1|EE023507
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|149073620|gb|EE161922.2|EE161922
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATTTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|148965176|gb|EE015985.2|EE015985
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|78075700|gb|DV504134.1|DV504134
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|149034778|gb|EE155078.2|EE155078
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|60401015|gb|DN233822.1|DN233822
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|78081105|gb|DV509517.1|DV509517
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|71756919|gb|DR954856.1|DR954856
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|211013387|gb|FL466952.1|FL466952
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|78122373|gb|DV540757.1|DV540757
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
EST: gi|86471665|gb|DY238035.1|DY238035
EST:     TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAG                         GAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC
genomic: TCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctatt ... gctcctgcagGAATACTTTTATGGGATTGCAAATGATCTTGCACCGCACTCAAACATTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCAAGTCCAACATTGATGTTGTAAAACTTCATAAATCAGAGGGTGTTGTCCTCAGAAATTCAAAATATCGGCAAAGAACGAGAAGCTTCCGAATCAAGgtaagctattttttttctggaataggtgaccagctatgctctcaaaaagacagaaccagtgttggcgggtcccacatgagtgggatctgaaaaaggaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaagg