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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgcatcttcttcaataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT

Basic information

species Zea mays
transcript GRMZM5G896082_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g64020.2 (Oryza sativa), 3'ss of exon 5
tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgca-tcttcttcaataa-tgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT
  |    |  |||     |     ||||| | ||  |  | | | |  |  |    ||  || |||  |     |||| | | ||||  | || || |||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||| |||| |||||  | ||||| || |||||  | || || |
-gtaaattctttttcctttcttccaattaattat--tcgactgactatttga----catgtttttcccc-----actcggtaatctttatgaacaaatgcagCTGCCAGAGCCTTTCGGTTTCATTTTCACATGGTTTGCTGCTTTGCCTCTAATATTGTTCATAGCACAGTCGATAACTAATGCCATAGTGAACGACTTCT

upper sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA05G03730.1 (Glycine max), 3'ss of exon 7
tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgcatcttcttcaat----aatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT
  ||| |   |  |     ||  ||||  ||    |||||  ||||    || ||    |   ||  |    | |      || || |  | |    | |||||||||| ||||||||  | ||||||||||| |||||||||||| | ||||| ||  |||   |||| | |||| | || || || || ||  | || ||| 
attcttcacatcacatagaaatgaaatagttt---cttaaa-cattaaagaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTAACAAATGCCATTGTAAAAGACTTTG

upper sequence: GRMZM5G896082_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 7
tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgcatcttcttcaat----aatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT
  ||| |   |  |     ||  ||||  ||      | || |||| |  || ||    |   ||  |    | |      || || |  | |    | |||||||||| ||||||||  | ||||||||||| |||||||||||| | ||||| ||  |||   |||| | |||| |||| || || || ||  | || ||| 
attcttcacatcacatagaaatgaaatagttt----cttagacattagaaaatattattacaattaatgcaattataacagatgttatgaattgttgagtgcagCTGCCGGAGCCTTTTAGTTTCATTTTCACTTGGTTTGCTGCTGTTCCCCTCATTGTGTGGATAGCTCTGTCACTGACAAATGCCATTGTAAAAGACTTTG

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|78114033|gb|DV532422.1|DV532422
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|50329133|gb|CO524259.1|CO524259
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|78112820|gb|DV531214.1|DV531214
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|91053496|gb|EB163914.1|EB163914
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|32849671|gb|CD989352.1|CD989352
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTATTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|78107801|gb|DV526219.1|DV526219
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|71325794|gb|DR799576.1|DR799576
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGC
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGC
EST: gi|148959398|gb|EC905432.2|EC905432
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAAAGCCTTTCGGATTCATTTTCACATGGTTGGCTG
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTG
EST: gi|71325792|gb|DR799575.1|DR799575
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|148949266|gb|EC894709.2|EC894709
EST:     GTTCTTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTC-TTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|78092904|gb|DV521278.1|DV521278
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|71449206|gb|DR830256.1|DR830256
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|74239749|gb|DT647663.1|DT647663
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|71773101|gb|DR971019.1|DR971019
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|149084782|gb|EE174281.2|EE174281
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|110522813|gb|EE026997.1|EE026997
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|93014353|gb|EB639873.1|EB639873
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|149097127|gb|EE182939.2|EE182939
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTTGCCCCT
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTT-GCCCCT
EST: gi|12046214|gb|BF728353.1|BF728353
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTATTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|13316197|gb|BG410644.1|BG410644
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|7135775|gb|AW498259.1|AW498259
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTATTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|149058763|gb|EE156781.2|EE156781
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTG
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTG
EST: gi|71322554|gb|DR797954.1|DR797954
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCTCT
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCC-CT
EST: gi|71775245|gb|DR973123.1|DR973123
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGAATCATTTTCACATGGTTTGCTGCTTTGCCC
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCC
EST: gi|78121212|gb|DV539596.1|DV539596
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|13516143|gb|BG518419.1|BG518419
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|149011246|gb|EE042332.2|EE042332
EST:     GTTCTTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGC
genomic: GTTCTTTTT-CATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGC
EST: gi|78107802|gb|DV526220.1|DV526220
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGAATCATTTTCACATGTTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|148949267|gb|EC894710.2|EC894710
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|71756718|gb|DR954655.1|DR954655
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
EST: gi|76908968|gb|DV163158.1|DV163158
EST:     GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAG                         CTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA
genomic: GTTCTTTTTCATTGATGAATTGACTGGTTTTGAGATCAATGTGTTCCAGgtcagtgtct ... aataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcaagatccacattcttcttctgctaactctgcatcttcttcaataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT
                        tgctaac  putative branch site (score: 1)
                                     tcttcttca  putative PPT
                                          ttcaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctgctggtttctggataaaaaaattattcatgcttaagtcattggtcaagatccacattcttcttctgctaactctgcatcttcttcaataatgcagCTGCCAGAGCCTTTCGGATTCATTTTCACATGGTTTGCTGCTTTGCCCCTAATATTGTTCTTAGCGCAGTCATTGACTAAGGCTATAGTCCAGGATTTTT

- tctgctg
- - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcatc