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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccttatcccatttaaaagagtagcggcatagcgattttgggggatttcacaacaagatctaactaaacagatcggatgcacttttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG

Basic information

species Oryza sativa
transcript LOC_Os05g23860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G435373_T01 (Zea mays), 3'ss of exon 1
cccttatcccatttaaaagagtagcggcatagc---gattttgggggatttcacaacaagatctaactaaacagatc---ggatgcacttttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
     || ||||||  |  |    |   |  |    | | || |  |  | ||    |||     | ||  ||  |    ||||    ||||| | | | ||  |||| ||||| ||||| || || |||||||||||||||||||||||||||||||||||||| |||
-----atgccatttttagaaccttccttaaggttttggtatttgaagtgtacatg-taagtatagaatattcacttttgaggatctggttttcgacgatattatagGTTTTGCATATGGACAGAAACGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAATCAG

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 1
cccttatcccatttaaaagagtagc--ggcatagcgattttgggggatttcacaacaagatctaactaaacagatcggatgcact--tttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
  ||||| |||||| | |   |  |      | | | | || |  |  |  |||   |  | ||   |  ||  || || |   |  |||| ||| | ||  |||| ||||| ||||| || ||||||||||||||||||||||||||||| ||||||||||| |||
--cttatgccattttagaaccttccttaaggttgtggtatttgaag--tctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G435373_T02 (Zea mays), 3'ss of exon 1
cccttatcccatttaaaagagtagcggcatagcgattttgggggatttcacaacaa-gatctaactaaacagatcggatgcacttttcaatg---tttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
          ||    |||   |   |       | |  |     ||   | |  | |   |   ||||  |||       | |||| | ||    |||| |||||  | ||||||||||| ||||| ||||| ||||||||||||||||| || ||||| ||||||
----agaaagatgcttaagttcaatagtcagcttactgcgttaacttgaccgatgatggattttttaaattgattttgaagaattttgagtgacgcttttacagGTTCTACACATGGATAGAAATGATTACTACGGAGGAGATTCCACCTCCCTAAACCTGAACCAG

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|88359659|gb|CI622349.1|CI622349
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88765626|gb|CI774720.1|CI774720
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|2310891|gb|C27046.1|C27046
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88399430|gb|CI606051.1|CI606051
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGAAGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88315062|gb|CI610121.1|CI610121
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88400779|gb|CI616784.1|CI616784
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58679926|gb|CK068613.1|CK068613
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|33655822|gb|CF278436.1|CF278436
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88425765|gb|CI571665.1|CI571665
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58600989|gb|CK011517.1|CK011517
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTG
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88421949|gb|CI611569.1|CI611569
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCAAATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88411859|gb|CI571351.1|CI571351
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTATTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88735490|gb|CI758998.1|CI758998
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58607180|gb|CK035213.1|CK035213
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGAGGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88392817|gb|CI624048.1|CI624048
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58673621|gb|CK062307.1|CK062307
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|33655650|gb|CF278264.1|CF278264
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88433375|gb|CI591815.1|CI591815
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88733282|gb|CI756459.1|CI756459
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|88726752|gb|CI750407.1|CI750407
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58668576|gb|CK057262.1|CK057262
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
EST: gi|58687035|gb|CK075722.1|CK075722
EST:     GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAG                         GTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTC

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: 75 (upstream exon), 58 (downstream exon)
Score: 24

GCCGCTCGCCGCCATGGATGAGGAGTACGACGTGATCGTGCTGGGGACGGGCCTCAAGGAGTGCATCCTCAGCGGCCTCCTCTCCGTCGACGGCCTCAAGgtacctctct ... gtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacaacaagatctaactaaacagatcggatgcacttttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
                aactaaa  putative branch site (score: 24)
                                            tgttttt  putative PPT
                                     ttttcaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccttatcccatttaaaagagtagcggcatagcgattttgggggatttcacaacaagatctaactaaacagatcggatgcacttttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - -gcggcat
- - - - - - - - - - - - - - - - - - - - - - - - - caacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa