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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttttttttttcgactgtgctccacatgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT

Basic information

species Zea mays
transcript GRMZM2G110143_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
----gtggttttttttttcgactgtgctccacatgtgg--ggattttg----gagcttct-atttttga---taattgtagattttttgg---gtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT
    ||    |||||||     | || | |   ||||   || ||| |    ||  |||| ||  ||||   | || ||   ||||||     ||||||| |||||||||||||||||||||||||||||||||||||| ||||| || |||||||| | ||||||
gtgcgtaacctttttttctttttttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
















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|4152004|gb|AI372138.1|AI372138
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGACG                         GCCGTAATGTGGATGGAAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|74237054|gb|DT644968.1|DT644968
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|149005364|gb|EE039916.2|EE039916
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211526332|gb|FL357659.1|FL357659
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|89757947|gb|DY687314.1|DY687314
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|149107293|gb|EE189175.2|EE189175
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|50328977|gb|CO524103.1|CO524103
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211277772|gb|FL330870.1|FL330870
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCANTGGTGCATGTTTGCAAAGTACGG
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCA-TGGTGCA-GTTTGCAAAGTACGG
EST: gi|211470092|gb|FL331953.1|FL331953
EST:     GCGGTACAAGTACGCCGACGAGSS-CAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATNGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71420359|gb|DR805069.1|DR805069
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71325769|gb|DR799565.1|DR799565
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211008119|gb|FL365557.1|FL365557
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGC
EST: gi|88752174|gb|DY536315.1|DY536315
EST:     GCGGTACAAGTACGCCGACGAGGGGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGA-CATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|71321797|gb|DR797591.1|DR797591
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|149101748|gb|EE287365.2|EE287365
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211347504|gb|FL349161.1|FL349161
EST:     GCGGTACAAGTACGCCGACRAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211440857|gb|FL253846.1|FL253846
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACG
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACG
EST: gi|211420441|gb|FL363214.1|FL363214
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211253499|gb|FL469937.1|FL469937
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|89756357|gb|DY686407.1|DY686407
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211235451|gb|FL353173.1|FL353173
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTT
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTT
EST: gi|60400418|gb|DN233225.1|DN233225
EST:     ATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: ATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|211208282|gb|FL335694.1|FL335694
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|31558121|gb|CD527333.1|CD527333
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGCAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|50335677|gb|CO530803.1|CO530803
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|74241218|gb|DT649132.1|DT649132
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|30307256|gb|CD001929.1|CD001929
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|74243434|gb|DT651348.1|DT651348
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|78105340|gb|DV523758.1|DV523758
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGA
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGA
EST: gi|78076983|gb|DV505417.1|DV505417
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|50328942|gb|CO524068.1|CO524068
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|76290040|gb|DV029608.1|DV029608
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
EST: gi|50325433|gb|CO520559.1|CO520559
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT
                         ttttgat  putative branch site (score: 4)
                                         tttttt  putative PPT
                   ttctatttttgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttttttttttcgactgtgctccacatgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG