Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaactctaaatctagtgatgatcggcacattattgtgtctatgcatgctacctttttcccttctaggattatacacttatcaatgttatttccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAAGGCAGAGGTGGCAAAATCGCAGAAGGCTTCTGGTAAAGGCAATGCTCCC

Basic information

species Oryza sativa
transcript LOC_Os07g12250.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12250.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 4
gaactctaaatctagtgatgatcggcacattattgtgtctatgcatgctacctttttcccttctaggattatacacttatcaatgttatttccataa-----cagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAAGGCAGAG---GTGGCAAAATCGCAGAAGGCTTCTGGTAAAGGCAATGCTCCC
          | |  |  |   | | | |   |    | ||| ||| | |  |||||        | | | |       |||| | || |   || |     |||||||||||||||| | ||||||||||| |||||||||||||| || |||||||  |||   |   ||||    |||||| |    |  || || |||      
---------gtttgtttctttcccgaagacagtcac-tatatacat-caatttttttttgaaactgaaatgtgattgattcaaagctaatctgatgattatgcagTGAGATCAAGGAGAGAATCAAGAAGACCAAGGACGAGAAGAAGGCAAAGAAGGTCGAGTATGCATCAAAGCAACAGAAGTCACAAGTGAAGGGAAATATC---
















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|55409773|gb|CV722149.1|CV722149
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88472849|gb|CI410120.1|CI410120
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|86522472|gb|CI162678.1|CI162678
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|33670740|gb|CF298979.1|CF298979
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88439396|gb|CI536368.1|CI536368
EST:     GGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: GGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88532023|gb|CI461478.1|CI461478
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|109711943|gb|CI029113.1|CI029113
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88381633|gb|CI682300.1|CI682300
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAG
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAG
EST: gi|15853700|gb|BI806496.1|BI806496
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAA-GGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88547591|gb|CI477897.1|CI477897
EST:     GAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: GAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|218483042|gb|FG956499.1|FG956499
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88906673|gb|CI375745.1|CI375745
EST:     CTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCCCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAATAAAGCCAAGAA
genomic: CTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88490990|gb|CI428262.1|CI428262
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88384109|gb|CI548450.1|CI548450
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTGG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|3767629|gb|AU031656.1|AU031656
EST:     GAGCTGAGAAGCCAGAGGTTCGTGATGGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: GAGCTGAGAAGCCAGAGGTTCGTGATG-CAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|55441469|gb|CV734055.1|CV734055
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|55435894|gb|CV731084.1|CV731084
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88514452|gb|CI441958.1|CI441958
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|3767630|gb|AU031657.1|AU031657
EST:     CTGAGAAGCCAGAGGTTCGTGATGCANCCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCNCATCAAGAAGACCAAAGGACGAGAAGAAAGCGAAGA
genomic: CTGAGAAGCCAGAGGTTCGTGATGCA-GCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGA-CAAAGGACGAGAAGAAAGCGAAGA
EST: gi|88485990|gb|CI423261.1|CI423261
EST:     TGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: TGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88511491|gb|CI438997.1|CI438997
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|112787065|gb|EE591987.1|EE591987
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAAGCCGCTTTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88383768|gb|CI545919.1|CI545919
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
EST: gi|88290337|gb|CI665126.1|CI665126
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGC
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGC
EST: gi|88574546|gb|CI666315.1|CI666315
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAA
EST: gi|163927613|gb|EG710753.1|EG710753
EST:     AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCG                         TGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA
genomic: AGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAA

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: 70 (upstream exon), 75 (downstream exon)
Score: 95

CGTACTCCCGGTCTATAGTTGGTGCTACCCTTGAAGTCATCCAGAAGAAGAGAGCTGAGAAGCCAGAGGTTCGTGATGCAGCAAGGGAATCCGCTCTTCGgtatgctatt ... tccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAAGGCAGAGGTGGCAAAATCGCAGAAGGCTTCTGGTAAAGGCAATGCTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacctttttcccttctaggattatacacttatcaatgttatttccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAAGGCAGAGGTGGCAAAATCGCAGAAGGCTTCTGGTAAAGGCAATGCTCCC
                                        ttatttcc  CT-rich tract
                               ttatcaatgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaactctaaatctagtgatgatcggcacattattgtgtctatgcatgctacctttttcccttctaggattatacacttatcaatgttatttccataacagTGAGATCAAGGAGCGCATCAAGAAGACAAAGGACGAGAAGAAAGCGAAGAAGGCAGAGGTGGCAAAATCGCAGAAGGCTTCTGGTAAAGGCAATGCTCCC

- - - - - - - -tgatgat
- - - - - - - - - - - - gcacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt