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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataagatccaaccctttatttattatgatgactctaagatctacagtactaataacatttttgacagcatctgacatattttgtcctgcgttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGCTTTCTGTGGAGGCCTTTCTCTTCCATCGTGTAGATCATGATCCGCTCTA

Basic information

species Oryza sativa
transcript LOC_Os10g06540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g06540.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149843_T02 (Zea mays), 3'ss of exon 3
---tataagatccaaccctttatttattatga--tgactctaagatctacagtactaataacatttttgacagcatctgacatattttgtcctgcgttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGCTTTCTGTGGAGGCCTTTCTCTTCCATCGTGTAGATCATGATCCGCTCTA
    |   | |  | |  ||| | |||| ||   || ||    |   || | |||||||   | || | || | | |||   | |||| |  |   || |||||| | ||||||||||| |||||||||| | || || |||||||||||  ||||||||||||||||||||||  |  |||| || |||||||||    | |  
aaagaattgctgtatctttttgtgtattgtggcctggctgcttgcaatatactactaat--taattcttacggtaactgtggtttttttttat---tttttgcagAGTTGTGTTGACAGTTGTCATAGTAGTGCTGCTCTACTTGATCATTTCTGCTTTCTGTGGAGGCCTTTCCTTGTCATCATGCAGATCATGAGTAACACAC
















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|5002912|gb|AU068021.1|AU068021
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|218487714|gb|FG953257.1|FG953257
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88281083|gb|CI402281.1|CI402281
EST:     CTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|86495637|gb|CI138270.1|CI138270
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|4715901|gb|AU057017.1|AU057017
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|86828469|gb|CI278586.1|CI278586
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88845762|gb|CI008759.1|CI008759
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|86253227|gb|CI058152.1|CI058152
EST:     GGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: GGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88549077|gb|CI478933.1|CI478933
EST:     CTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88845739|gb|CI008736.1|CI008736
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|86854443|gb|CI256565.1|CI256565
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|218501230|gb|FG958972.1|FG958972
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88486640|gb|CI423911.1|CI423911
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTAGTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88531449|gb|CI459926.1|CI459926
EST:     ATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: ATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|163927495|gb|EG709951.1|EG709951
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCA
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCA
EST: gi|86508036|gb|CI150669.1|CI150669
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88995513|gb|CI022836.1|CI022836
EST:     TTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: TTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88481749|gb|CI419020.1|CI419020
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|58676981|gb|CK065668.1|CK065668
EST:     CCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTTTACTTTACTTGATCATCGCTGC
genomic: CCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88560100|gb|CI490730.1|CI490730
EST:     GCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: GCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88258300|gb|CI360886.1|CI360886
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TACTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|86854474|gb|CI256596.1|CI256596
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|218489759|gb|FG952877.1|FG952877
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|89167265|gb|CI252796.1|CI252796
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88508225|gb|CI435731.1|CI435731
EST:     CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|88982000|gb|CI027577.1|CI027577
EST:     CTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: CTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
EST: gi|89175386|gb|CI042407.1|CI042407
EST:     GAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCT                         TGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC
genomic: GAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGC

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: 71 (upstream exon), 69 (downstream exon)
Score: 29

TCGTCGACAAGACCTCCACCATGCAAGACAGTGCTTTCCACTTCCGCAAGCAATCCAGGAGGCTCAGGAGAGCTCTTTGGATGAAAAATGCCAAGCTTCTgtaagtcacc ... gttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGCTTTCTGTGGAGGCCTTTCTCTTCCATCGTGTAGATCATGATCCGCTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtactaataacatttttgacagcatctgacatattttgtcctgcgttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGCTTTCTGTGGAGGCCTTTCTCTTCCATCGTGTAGATCATGATCCGCTCTA
     taataacatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataagatccaaccctttatttattatgatgactctaagatctacagtactaataacatttttgacagcatctgacatattttgtcctgcgttgttgcagTGCTGTGTTGACAGCTGTCATAGTACTTCTACTTTACTTGATCATCGCTGCTTTCTGTGGAGGCCTTTCTCTTCCATCGTGTAGATCATGATCCGCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA