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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaacctaatgtacttcatcatgggattttgttgtagttgtagaaagaactcaaaatgtataattgttgttacaataagtat...

Basic information

species Oryza sativa
transcript LOC_Os07g26940.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G558324_T01 (Zea mays), 5'ss of exon 3
ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaac-ctaatgtacttcatcatgggattttgttgtagt-tgtagaaagaactcaaaatgtataattgttgttacaataagtat-
|||| || || ||||||  | | ||||||||||||||||| ||||| ||  | || ||||||||||||||||||||| | | ||| || | ||| || |||||||| |     ||||   | | ||  |  | |||||  |     | | | |   | | ||| |  ||    |  || |||  |    | | |||   |   
ACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCAAACAGCTTACTCGTAATAGGAAGTTCCTCATTGTTGTTCATGTTGTCCTgtaagtgctg--cccatcgtatctctgttcaatttcattttcattctctatggctatgtttaggagaaatattatgtg-atagatacactcaaaatgtttgct

upper sequence: LOC_Os07g26940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaacctaatgtacttcat-catgggattttgttgtagttgtagaaagaactcaaaatgtataattgttgttacaataagtat---------
||||||||||||||| |||| | || |||||||| |||||||| || || ||||| |||||||| || || ||||| ||||||||||||||||||||||||||||||||||       ||| ||| ||| | ||||  |||   |||    | ||| |   | ||       |||| |||| |  |   | ||   |||||         
ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatc------tcatcctcatgcagttcacacatcaaattgctctttaggttctgcaaagg----aaatttatactaatcagttcaggcagtatttgcttgtg

upper sequence: LOC_Os07g26940.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064898_T02 (Zea mays), 5'ss of exon 2
ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaacctaatgtacttcatcatgggattttgttgtag-ttgtagaaag-aactcaaaatgtataattgttgttacaataagtat--
||||||||||||||| |||| | || |||||||| |||||||| || || ||||| |||||||| || |||||||| || ||||||||||||||||||||||||||||||| || ||        | |  ||  ||| |    |||    | ||| || | ||||| || | || |   || | |   |   || |   | |  
ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttccatctc-atcctcttgcagttcaca-catgaacaaattactctttagattctggaaaggaaattaatactaatcagtacag--gcagtggttgttt

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|86537135|gb|CI177341.1|CI177341
EST:     TGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCGATGCTTTTCCT
genomic: TGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|33661039|gb|CF292006.1|CF292006
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86254897|gb|CI017017.1|CI017017
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88216129|gb|CI215978.1|CI215978
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88833765|gb|CI077246.1|CI077246
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86824161|gb|CI260782.1|CI260782
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86885436|gb|CI318587.1|CI318587
EST:     ACTTACTCGTAATAGGAAGTTCTTGACTGTTGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: ACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|58589386|gb|CF987694.1|CF987694
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGATTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|87031947|gb|CI268176.1|CI268176
EST:     AAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: AAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|89168674|gb|CI038526.1|CI038526
EST:     TACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGTTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: TACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|89165133|gb|CI255190.1|CI255190
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86423317|gb|CI060890.1|CI060890
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|7273861|gb|AU083405.1|AU083405
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGNCTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|33817767|gb|CF334716.1|CF334716
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|89169423|gb|CI038432.1|CI038432
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCGATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88203460|gb|CI203309.1|CI203309
EST:     GGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: GGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86530598|gb|CI170804.1|CI170804
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|58589564|gb|CF987872.1|CF987872
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGATTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86854124|gb|CI252115.1|CI252115
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|7273849|gb|AU083393.1|AU083393
EST:     ACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: ACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88204332|gb|CI204181.1|CI204181
EST:     AGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: AGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|14714226|gb|AU198157.1|AU198157
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|58677711|gb|CK066398.1|CK066398
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88216873|gb|CI216475.1|CI216475
EST:     AGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: AGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86524912|gb|CI165118.1|CI165118
EST:     TTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: TTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86855483|gb|CI267012.1|CI267012
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|7273842|gb|AU083386.1|AU083386
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86424115|gb|CI062876.1|CI062876
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|87025204|gb|CI265769.1|CI265769
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTCCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|87010615|gb|CI283690.1|CI283690
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|86253569|gb|CI014202.1|CI014202
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
EST: gi|88216784|gb|CI216633.1|CI216633
EST:     CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCT                         GTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT
genomic: CAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCT

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), 73 (downstream exon)
Score: 67

ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... tttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCTCAACACCATTGCAGTTCTGGTACTAGTGGTAGCAAAGCTGCCAAACATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaacctaatgtacttcatcatgggattttgttgtagttgtagaaagaactcaaaatgtataattgttgttacaataagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaagaa