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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaggatatttctgaacagcatagggagggaagacaatatactacaatacatgactgcgttactctttccgcttttgtacgtaattggcaatttctccctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g22330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22330.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G158662_T01 (Zea mays), 3'ss of exon 2
gtacaggatatttctgaacagcatagggagggaagacaatatactacaatacatgactgcgttactctttccgctt--ttgtacgtaattggcaatttctccctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG
                              | | |  | |   ||| ||  || |  | |   | | | |    ||  ||||   |||||      |||||  || |  |||||||||||| |  || |||||||||||||||  ||||||||||||||||||||| ||||||||||||||||| || ||||| |||||||||||||||||
------------------------------gtatgcaagttcgcta-aacccaagttt-caccattatataaatttgtttgtctataattaagtgattctct-tcttcccagAGCAATTCCTTTTGGGTCAACACCCAAGAATAATGATGGCACATCTGATGCTGGAACAAATTGGTTAATGTTTGAGTTGCTGTGGAGAGATTTCTTCAG
















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|29616243|gb|CB621255.1|CB621255
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|86480762|gb|CI123395.1|CI123395
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATCCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|29616242|gb|CB621254.1|CB621254
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88994060|gb|CI116024.1|CI116024
EST:     AGCATGCTTCAAG                         AGCAATTCCATCGGGATCGACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: AGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88250922|gb|CI248773.1|CI248773
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88263632|gb|CI367406.1|CI367406
EST:     GTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: GTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|25799829|gb|CA755790.1|CA755790
EST:     TGCCTCTCACCGCGCTTCATGTATGATGAGTTGAGGAAGCATGCTTTAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|27578008|gb|CB000703.1|CB000703
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|86429391|gb|CI076072.1|CI076072
EST:     TGCCTCTCACCGCGCTTNATGTATGAGGAGTTGAAGGAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|38568777|gb|CD670992.1|CD670992
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|38480046|gb|CF964135.1|CF964135
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88245986|gb|CI245835.1|CI245835
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88228080|gb|CI227560.1|CI227560
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88199863|gb|CI199713.1|CI199713
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|88222823|gb|CI220888.1|CI220888
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|33800287|gb|CF326012.1|CF326012
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|27576543|gb|CA999237.1|CA999237
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|86505349|gb|CI147982.1|CI147982
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|86493833|gb|CI136466.1|CI136466
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
EST: gi|300215532|gb|HO088158.1|HO088158
EST:     TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAG                         AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC
genomic: TGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 72 (downstream exon)
Score: 55

TATATGGTGCTAATTTCTCCTGCAAAATTTCACCATGGCTTGCTACAGGTTGCCTCTCACCGCGCTTCATGTATGAGGAGTTGAAGAAGCATGCTTCAAGgtacaggata ... ctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcgttactctttccgcttttgtacgtaattggcaatttctccctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG
                                      tttctccctcattac  CT-rich tract
                   ttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaggatatttctgaacagcatagggagggaagacaatatactacaatacatgactgcgttactctttccgcttttgtacgtaattggcaatttctccctcattacagAGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA