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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttttttttttcgactgtgctccacatgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA

Basic information

species Zea mays
transcript GRMZM2G110143_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
----gtggttttttttttcgactgtgctccacatgtgg--ggattttg----gagcttct-atttttga---taattgtagattttttgg---gtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA------------------------
    ||    |||||||     | || | |   ||||   || ||| |    ||  |||| ||  ||||   | || ||   ||||||     ||||||| |||||||||||||||||||||||||||||||||||||| ||                        
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|211440859|gb|FL253848.1|FL253848
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA
EST: gi|211008119|gb|FL365557.1|FL365557
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGC
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGC
EST: gi|211235451|gb|FL353173.1|FL353173
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTT
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTT
EST: gi|211470092|gb|FL331953.1|FL331953
EST:     GCGGTACAAGTACGCCGACGAGSS-CAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATNGGAGGAACATCATGGTGCAGTTTGCAAA
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA
EST: gi|78105340|gb|DV523758.1|DV523758
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGA
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGA
EST: gi|211440857|gb|FL253846.1|FL253846
EST:     GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATG                         GCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA
genomic: GCGGTACAAGTACGCCGACGAGGCGCAGAAGGCTATAGATCGGCTCGATGgtggtttttt ... ttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA
                         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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttttttttttcgactgtgctccacatgtggggattttggagcttctatttttgataattgtagattttttgggtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA