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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcttgttggatttttttgcacctctctatcctcttgctgtgtagctaaaatgcttttactctttataacttatgccctagcgctgtgttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------------ttttgcttgttggatt-tttttgcacctctctat-cctcttgctgtgtag-----ctaaaatgct-tttactctttataa----cttatgccctagc---gctgtgt-----------tcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG
                                                               | ||| || | |  ||   |||   | |   ||| |||| | | | | |       ||| | ||  |||| | ||   ||    | |   | ||  |   | | | |           | |||||||||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || ||||||||||| || ||||||||||||||
gtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG

upper sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------ttttgcttgttggatttttttgcacctctc---tatcctcttgctgtgtagctaaaatgcttttactctttataacttatgccctagcgctgtgttcttgt--agGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG
                ||  |||  |  | ||   | ||     |    ||  | | |||   |  ||||  | |||   ||    || |||   |    | |    | || |  |  |||| ||||  ||||| |||    | |||||||||||||||||| ||||||||||  | ||  |||||||||| || |||||||| ||
gtatataatatacctcttgactttgtatagttacctccattaaacagacattatttggctccttttctaatct-cttaacctgagaatgactccagtttgatccactttttttcatccagGGGGCAAAAGATGAGTTTACTCTTGATCTTGTCGAGCAATGTTCGTTTCAGAAAGAGCGCGTAATGCACCTCGTCATGACATCGAG
















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|71421501|gb|DR805467.1|DR805467
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|32837204|gb|CD976882.1|CD976882
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGT
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGT
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAA
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|50325446|gb|CO520572.1|CO520572
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|211276223|gb|FL230638.1|FL230638
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGGCACCCTGAGgtatgtgtta ... gttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctaaaatgcttttactctttataacttatgccctagcgctgtgttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG
                     ttataac  putative branch site (score: 2)
                                            tgttctt  putative PPT
            ttttactctttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcttgttggatttttttgcacctctctatcctcttgctgtgtagctaaaatgcttttactctttataacttatgccctagcgctgtgttcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA