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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcatatagttactgttatcttttgcaatctcatcaatttcattatacaaaagagtcaaagctgttattttggtggacctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g03260.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 10
ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcatatagt-tactgttatcttttgcaatctcatcaatttcattatacaaaagagtcaaagctgttattttggtggacctgcag
|||| ||||||||||||||||||||||||| ||| ||||||||||  |||||||||| |||| || |||| |  |||||||||   |  |    |   |||   |||| |||     | ||||  | | |    | || ||||||
ATTTTTTAGTGACTACCGGTTTGATGTATCGAAACTGGAGCCAGTAGTTGCCAAGgtctgttgatgtagtattttgttatcttcatc--ttctgttgcttttcctataaaaa-----cgaagcaataactgcctttgatctgcag

upper sequence: LOC_Os02g03260.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 10
ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcatatagttactgttatcttttgcaatct-catcaatt--tcattatacaaaagagtcaaagctgttattttggtggacctgcag
|||| |||| |||||||||||||||||||| ||| ||||||||||  |||||||||||||||     |       |||| || |||||||  ||||  ||  |  || | | | | |  |||||   |   | |  |||||||||||
ATTTTTTAGCGACTACCGGTTTGATGTATCAAAACTGGAGCCAGTAGTTGCCAAGgtttgttggcgca-------ttattttctgcaatcgacatcttttgttggttttcctataaaaacaaaggaatacctgtcttggacctgcag
















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|33689599|gb|CF317838.1|CF317838
EST:     GTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: GTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|88340371|gb|CI659577.1|CI659577
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAG
EST: gi|29677182|gb|CB673457.1|CB673457
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|218494441|gb|FG968569.1|FG968569
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|58666580|gb|CK055266.1|CK055266
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|88336267|gb|CI648854.1|CI648854
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTG
EST: gi|29658442|gb|CB654717.1|CB654717
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|29628819|gb|CB633830.1|CB633830
EST:     TAGTGACTACCCGNTTTGATGTATCCAAATTGGAGCCAGTTGTTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TAGTGACTA-CCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|2312204|gb|C28359.1|C28359
EST:     TAGTGACTACCGGTTTGATGTATNCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTCCAA-GATGTCAAG
genomic: TAGTGACTACCGGTTTGATGTAT-CCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|29636583|gb|CB641592.1|CB641592
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|88329810|gb|CI651478.1|CI651478
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACC
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACC
EST: gi|88571723|gb|CI663096.1|CI663096
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAA
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAA
EST: gi|29616438|gb|CB621450.1|CB621450
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|218490400|gb|FG966882.1|FG966882
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAG
EST: gi|29628818|gb|CB633829.1|CB633829
EST:     TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTGTTGCCAAG                         CCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAA
genomic: TTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAA

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: 69 (upstream exon), 54 (downstream exon)
Score: 50

ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcat ... ggacctgcagCCACATTCACCTGACAACCGTGCTCTAGCAAGAGAGTGCAAAGATGTCAAGATTGACCGGGTCTATATCGGTTCTTGTACTGGAGGTAAAACTGAGGACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGCCAAGgtttgttcatatagttactgttatcttttgcaatctcatcaatttcattatacaaaagagtcaaagctgttattttggtggacctgcag

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