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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtctgcttaataatttcagaacttgctctatttttgtgcctgcagtgcttttaagcatatggttgcaattttgacattttgtcgtgatctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA

Basic information

species Zea mays
transcript GRMZM5G814700_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 14
aatgtctgcttaataatttcagaacttgctctatttttgtgc---ctgcagtgcttttaagcatatggttgcaa--ttttgacattttgtcgtgatctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA
|    ||  |   | |  || |||     | |  ||   |||    |||  | | |||||  ||||| ||   |  ||||| | |||||| ||        | ||||||| ||||| |||||| ||||||||||||||||||| |||||||| ||  |||| || || |||||||  ||||| ||||||   |    || |   |
agaaccttttatgttagctctgaaaggtttattgttccatgcagattgctattcctttaactatatgattaacaccttttgtccttttgttgt-----ccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGAGCTTCCTCTGGCGAAGAAAGCCACCAGGACATCTCAATCACCTCGGTTA
















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|22542340|gb|BU092793.1|BU092793
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|22472602|gb|BU037082.1|BU037082
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|26558461|gb|CA830696.1|CA830696
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
EST: gi|33093066|gb|CF053060.1|CF053060
EST:     GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAG                         GAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG
genomic: GCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttat ... tctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgcttttaagcatatggttgcaattttgacattttgtcgtgatctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA
                          ttttgac  putative branch site (score: 3)
                                             tctttctc  putative PPT
                        aattttgacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtctgcttaataatttcagaacttgctctatttttgtgcctgcagtgcttttaagcatatggttgcaattttgacattttgtcgtgatctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA