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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
tcatgtaatgtaagattttactttga-agtttggatagtagcac--agataccatttttctgtttgcttgtgatctaattacgttcctcatttca-tatga-----cagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT
        ||  ||||| || | ||| | |||| ||   |       |||||| |   | |  ||  ||  | ||| |       | |  ||||| | |||     ||||||||||| ||||||||||||||||||||||| | ||| ||||| |||||||| ||||| ||||||
--------tgctagattctattgtgacactttgaatgtcattttctggatacc-tgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 9
--tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT
   |     ||||||| | ||  |   || | |      |   |    | | |    |    |  |  |   | |   |    |||| ||||  | |  |||||||| || |||||||||||||||||||||||  |||| |||||||||||||| |  || || |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactgac--gacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G04320.2 (Glycine max), 3'ss of exon 9
--tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT
   |     ||||||| | ||  |   || | |      |   |    | | ||   |    | | |  || | |  ||   | ||| ||||  | |  |||||||| || |||||||||||||||||||||||  |||| |||||||||||||| |  || || |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgctatagcttcact-gatgatgcttttcttttat-cctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 9
----tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT
    |  || ||  | | |||  |      | ||   ||     |      | || | ||        | |||  ||||||  | || |||  | || |  ||||| || || ||||| || ||||||||||||||  |||||||||||||||| ||||||||||| |||
ttattgttggaaaatgaaattcaagc--acaattgaaattccttctattcaaacagtgtttaaacaattggtg--ctaatttggatcatcaaatgatgttgcagACTGTTGATGAGATTTATAAGGTTGCATCAATATCACTCAGTCCAAATGTCCCTGGGCAGATATTT

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|58658560|gb|CK047240.1|CK047240
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|29671704|gb|CB667979.1|CB667979
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33381539|gb|CF196882.1|CF196882
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33381769|gb|CF197112.1|CF197112
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCNNNTGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|29645692|gb|CB650699.1|CB650699
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|58688608|gb|CK077295.1|CK077295
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCAGTCAATCGCACTCAGTCCAAATGT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCA-TCAATCGCACTCAGTCCAAATGT
EST: gi|13420573|gb|AU174663.1|AU174663
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|29615822|gb|CB620834.1|CB620834
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33381622|gb|CF196965.1|CF196965
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33665284|gb|CF296251.1|CF296251
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAAGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33801487|gb|CF326616.1|CF326616
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|88357956|gb|CI650692.1|CI650692
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCA
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCA
EST: gi|58588206|gb|CF986514.1|CF986514
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33381833|gb|CF197176.1|CF197176
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTC
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTC
EST: gi|33675257|gb|CF303496.1|CF303496
EST:     NGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: -GTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|5667553|gb|AU077813.1|AU077813
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|313079823|gb|HO213262.1|HO213262
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|701822|gb|D48113.1|D48113
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|33381462|gb|CF196805.1|CF196805
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|11442608|gb|BF430511.1|BF430511
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|29689279|gb|CB685554.1|CB685554
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
EST: gi|38479882|gb|CF963971.1|CF963971
EST:     AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAG                         ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT
genomic: AGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTT

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: 73 (upstream exon), 75 (downstream exon)
Score: 166

GGAAGTTCAGCTGGTTTCTTTCCATACTGTGTCAAAAGGATATTGGGGGGAGTGTGGACAACGTGGAGGGTATTTTGAAATGACAAATCTTCCTCCCAAGgtgatgccat ... catatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT
                        atctaat  putative branch site (score: 166)
                                   ttcctcatttc  putative PPT
                        atctaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgtaatgtaagattttactttgaagtttggatagtagcacagataccatttttctgtttgcttgtgatctaattacgttcctcatttcatatgacagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
-catgtaa