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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttgatggcaaggttgaatttgtattacttagtcactagggggtgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT

Basic information

species Zea mays
transcript GRMZM2G314679_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 3
aggttgatggcaaggttgaatttgtat-tacttagtcactagggggtgtcgactctccag--aaat----aaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT
   |  |||  |   ||   | |  || ||   | |     |    | |  | |||  ||   |||    || ||  |  |||| | | ||||| | |||| | ||||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||  |
---tcaatgttataattatgtctcgatatatccacttttctga---tctttattctttagttgaatttggaattttcctttgatacctgtttttgg-ttctctccagCTGAGATAACATTGTTTGATGGCTATATTGTCGTTTATAAGTTTGTACAAGACCTTCATTTTTTTGTCACCGCTGGTGATGATGAGAATGAGCTCATTAT

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G13190.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------aggttgatggcaaggttgaatt-tgtattacttagtcactagggggtgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT
                                                                                          || ||| ||   |   ||| || | ||| ||    |          ||| || | |   ||  | | || |      | | |   ||||     ||| |||| || ||| || |||||||   | | |||||  ||||||||||||| || || |||||||| ||||| |||| ||| ||| |||| |||||||| |||||
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatca--ctgatttgtatatgaccccattttgtaaacatgttgagtgtt--gacttcatttttattgcctccttgggttttttcattttacagCAGAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------aggttgatggcaaggttgaatttg--tattacttagtcactagggggtgtcgactctccagaaataaattc-tccctgatgc----atattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT
                                                                                  |  ||        | |||   | |  |  |  | | | | | |    || |  |  |  || | | | ||| |  ||  |||    ||    |||     ||  |||| || ||| || |||||||   | | ||||| |||||||||||||| || || |||||||| ||||| |||| ||| ||| |||| |||||||| |||||
gtgtgtaaaacttatgtgatatggtcaatgatcaattgaccatgccataattcatgatgaagaattgtctgtgtgtttgatcaaattctgtatgtgattgggatagattgctgatcactgattcgtatatgacctcctttgagtattgacttcatttcttttgccttcatgggctttttcatttgacagCGGAAATAGCAATGTTTGAGAATAACATTGTTGTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTT

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------aggttgatggcaaggttgaatt-tgtattacttagtcactagggggtgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT---
                                                                                          || ||| ||   |   ||| || | ||| ||    |          ||| || | |   ||  | | || |      | | |   ||||     ||| |||| || ||| || |||||||   | | |||||  ||||||||||||| || || |||||||| ||||| |||| ||| ||| |||| |||||||| |||||   
gtgtgtaaaacttctgtgatatggtcaataatcaattgaccatgccataattcatgatgtgtttggtcaaattctgtctgtgattgtgatagattgctgatca--ctgatttgtatatgaccccattttgtaaacatgttgagtgtt--gacttcatttttattgcctccttgggttttttcattttacagcagAAATAGCAATGTTTGAGAATAACATTGTTCTTTACAAGTTTGTCCAAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGC

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|31357552|gb|CD441909.1|CD441909
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184335|gb|FL140041.1|FL140041
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGKACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|60356728|gb|DN223701.1|DN223701
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211181937|gb|FL140035.1|FL140035
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGAT
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGAT
EST: gi|87157301|gb|DY402090.1|DY402090
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|7137590|gb|AW499170.1|AW499170
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184344|gb|FL140050.1|FL140050
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|15313043|gb|BI478532.1|BI478532
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184341|gb|FL140047.1|FL140047
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|5296305|gb|AI783075.1|AI783075
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|22819508|gb|BU499598.1|BU499598
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|56382683|gb|CV985352.1|CV985352
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184337|gb|FL140043.1|FL140043
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211344197|gb|FL190861.1|FL190861
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184338|gb|FL140044.1|FL140044
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|62550301|gb|DN830721.1|DN830721
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|5928724|gb|AW055941.1|AW055941
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|5901227|gb|AW042327.1|AW042327
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGGTATATTGTCGGTTACAAGGTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|6227104|gb|AW155808.1|AW155808
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211181941|gb|FL140039.1|FL140039
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCG
EST: gi|211181938|gb|FL140036.1|FL140036
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184339|gb|FL140045.1|FL140045
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|33103253|gb|CF063213.1|CF063213
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211181939|gb|FL140037.1|FL140037
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCNCGGACAGAAG                         CTGAGATAACATTG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTG
EST: gi|211181940|gb|FL140038.1|FL140038
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
EST: gi|211184343|gb|FL140049.1|FL140049
EST:     CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAG                         CTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG
genomic: CGAAAAGTCTGTTTTTACTAAAACTCTAAAGACAAATGCACGGACAGAAGgtatttttca ... ttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT
                         ccctgat  putative branch site (score: 4)
                                   tattttttgcttcttt  putative PPT
            agaaataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttgatggcaaggttgaatttgtattacttagtcactagggggtgtcgactctccagaaataaattctccctgatgcatattttttgcttctttgcagCTGAGATAACATTGTTTGATGGTTATATTGTCGTTTACAAGTTTGTACATGACCTTCACTTTTTTGTCACCGCTGGAGATGATGAGAATGAGCTCATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA