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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatctttcattcaatacctgaacactagttagatcttaacggaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG

Basic information

species Zea mays
transcript GRMZM2G087598_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087598_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 2
ttcatctttcattcaatacctgaacactagttagatcttaacggaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG
|| |  | || || | |      | | |    |  |  | |     |||| |        ||  ||||||  | | ||| |||| ||| |  || |||||||   ||| || |||||||||||||| ||||||||||||||||| || ||||| |||||||||||||| || ||| ||||||| |||||||| |||||||
ttgagttatctttgagtgttctcaaagttagaattttgttatcctcatatgtccaaaaccttgctaacattatggatataccttttaacttgttgcacagGTAAGTGTTGATGTTCCTGATGTACGCGGAAGGACAGAGATTCTTAAGGTGCACGGTAGCAACAAGAAGTTCGATACTGATGTCTCTCTTGAAGTCATAG

upper sequence: GRMZM2G087598_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 2
ttcatctttcattcaatacctgaacactagttagatcttaacg-gaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG
                             ||  |||  ||    |||||   |   | || || | ||    |    ||       | |||  ||   |||||| | || || ||||| ||| || | |||||||| || || ||||| || |||| ||||||||| || |||||| |||||||||||||||| || || |
-----------------------------gtatgattatattatgaaatgcctcatgctt-ttgtgaatgagtaaattactaaacatcattgctttttcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG

upper sequence: GRMZM2G087598_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 2
ttcatctttcattcaatacctgaacactagttagatcttaacggaaata-tatgggggttgttcttaacatctttggt---atgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG
                         | |  |||  |  | |      || |      |||  |  | | ||   ||     |       | | |  ||   |||||| | || || ||||| ||| || | |||||||| || || ||||| || |||| ||||||||| || |||||| |||||||||||||||| || || |
-----------------------gtattgattatgttatgaaatgcctaatgcttttgttaatgattaaattactgaacaaaaaaaacatcaatgcttttgcagGTGACAGTTGATGTTCCAGATATAAGGGGAAGGACTGAAATCCTAAAGGTTCATGCTAGCAACAAAAAGTTTGATGCTGATGTTTCTCTTGAAGTGATTG

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|13178243|gb|BG349501.1|BG349501
EST:     TGACATATTGGATTCCGGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGGATTCTAAAAGT
genomic: TGACATATTGGATTCCG-CTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAG-ATTCTAAAAGT
EST: gi|211259405|gb|FL294935.1|FL294935
EST:     CTGACATCTTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
EST: gi|13178244|gb|BG349502.1|BG349502
EST:     CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTA
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTA
EST: gi|76011446|gb|DT938616.1|DT938616
EST:     CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
EST: gi|194717144|gb|FK934297.1|FK934297
EST:     CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTAC
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTAC
EST: gi|13316150|gb|BG410597.1|BG410597
EST:     CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
EST: gi|32850222|gb|CD989903.1|CD989903
EST:     CTGACATCTTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAG                         GTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG
genomic: CTGACATATTGGATTCCGCTTTACTTAGACCTGGGCGTTTTGATAGACAGgtttgttatt ... cattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG
                tcttaac  putative branch site (score: 2)
                                        taattcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatctttcattcaatacctgaacactagttagatcttaacggaaatatatgggggttgttcttaacatctttggtatgccttgtaattcattacacagGTGTCTGTCGACGTTCCTGATGTACGTGGAAGGACAGAGATTCTAAAAGTGCATGGTAGCAACAAGAAATTTGATTCTGATGTTTCTCTTGATGTCATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA