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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggactccatcatcttacctttccatttctcatggttatggtggatgatcttttaactgttatatatacttttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG

Basic information

species Oryza sativa
transcript LOC_Os11g28340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------gtatgg-actccatcat-----cttacctttccatttctcatggttatggtggatgatcttttaactgttatat--atacttttgttg---cagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG
                                                    | |    | | ||| |       || |  | ||  || |  | | | |    | |  || |  | |  || | |   |  |||| ||    |||| ||| | || || || ||||| ||||| |||||||||||||||||||  ||||||||||||||
gtatgaattccttgtgccatccatttttattccttgaatgtgattcggagccgcacattatttcattaaagatgtttgcactccccattatggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG
















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|117216901|gb|CT861591.1|CT861591
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88476998|gb|CI414269.1|CI414269
EST:     AGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: AGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88849104|gb|CI087626.1|CI087626
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88555052|gb|CI485279.1|CI485279
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88528582|gb|CI456828.1|CI456828
EST:     CGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: CGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86542052|gb|CI182258.1|CI182258
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86529172|gb|CI169378.1|CI169378
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|426840|gb|D22915.1|D22915
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86886118|gb|CI321154.1|CI321154
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|27546640|gb|CA764760.2|CA764760
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88262756|gb|CI366530.1|CI366530
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GGTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86870391|gb|CI319497.1|CI319497
EST:     GATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGGCTGACTTCTTCTAC
genomic: GATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTAT-GCTGACTTCTTCTAC
EST: gi|88533140|gb|CI460677.1|CI460677
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88241404|gb|CI241253.1|CI241253
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88541507|gb|CI470782.1|CI470782
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|33691459|gb|CF319698.1|CF319698
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|86545642|gb|CI185848.1|CI185848
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88529756|gb|CI458100.1|CI458100
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|89187774|gb|CI009758.1|CI009758
EST:     TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
EST: gi|88439304|gb|CI536276.1|CI536276
EST:     TACTTCACTGAGCCCCATTTCGTTCATTGGATAA                         GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT
genomic: TACTTCACTGAGCCCCATTTCGTTCATTGGATAAgtatggactc ... tttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcatggttatggtggatgatcttttaactgttatatatacttttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG
                         ttttaac  putative branch site (score: 2)
                                           cttttgtt  putative PPT
                         ttttaactgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggactccatcatcttacctttccatttctcatggttatggtggatgatcttttaactgttatatatacttttgttgcagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG