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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatctagcaatgacacttatgtatgaaactgaactgaatacgacaaggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCAC

Basic information

species Zea mays
transcript GRMZM2G030280_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------aca-tctagcaatgacact----tatgtatgaaactgaactgaatacgaca-aggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCAC
                                                            | | |||    ||| |  |    ||||||  |  | ||   || ||    | ||  |||  |   || | ||||||||  |  |  | |    | ||||    ||||||||||||||||||| ||||||||| ||||||||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| ||||||||||| |
gtaccatgttttttctctctctctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtac-taaatcctctttatcttttccactatatg----aagGCTGACAACCTGCGGCAGCAGACTCTTCAACAGATGCAAAGGATACTGACCACTAGGCAGTCTGCCCGTGCGCTTCTTGTGATAAGCGATTACTCTTCGC
















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|89106576|gb|DY576793.1|DY576793
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCTTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|89106563|gb|DY576780.1|DY576780
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|71426015|gb|DR807065.1|DR807065
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTTTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|19351176|gb|BM895708.1|BM895708
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|19437057|gb|BM953467.1|BM953467
EST:     TGGCCATGGCTATGGGAAAACTCGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|71305564|gb|DR788925.1|DR788925
EST:     TGGCCATGGCTATGGGAAAACTTGGATCGCTTGAGAATTTCCTTTGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|19437027|gb|BM953437.1|BM953437
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGG
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGG
EST: gi|76290000|gb|DV029568.1|DV029568
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAA-TTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|22490996|gb|BU050919.1|BU050919
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
EST: gi|19351209|gb|BM895741.1|BM895741
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         GCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... atgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCAC
                gcctaaa  putative branch site (score: 3)
                                            tatgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatctagcaatgacacttatgtatgaaactgaactgaatacgacaaggacaacctgcggtgcctaaatcctgctacttctctttgttgtatgtatcaagGCTGACAACCTGCGGCTGCAGACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - -atgtatg
- - - - - - - - - - - - - - - tgaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -cctgcgg