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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttcctgttgtttttctcaccctgctcatcttgcttcaatagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG

Basic information

species Oryza sativa
transcript LOC_Os02g51790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G811409_T01 (Zea mays), 3'ss of exon 1
-tttttttc----ctgttgtttttctcac-cctgctcatcttgcttcaatagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG---------
 | |  | |    | | | |||||| ||| || ||||| |    ||  | |     ||| | |   ||    | |||||   |   |            |||| |   |  |      | ||  |  |||| |||  ||||||||||||||||||| ||||||||||||| |||||||||||| | |||||||||||| ||||| |         
gtatcgtacaaaaccgatttttttcccactcccgctcaac---atttgaaactgttttttttcccactccgctcagcataagcagagaa----------gcat-atgctatttagGAACAGAAGGCAAAAACAGAGAGGGAAATTGAACAAGGAATAAACAAGAGATTGTATAGGAAGCTTGATACGAAATGGAAGCAGAGCATTGTGGTCAGAC

upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G159554_T01 (Zea mays), 3'ss of exon 1
----tttttttcctgttgtttttctcaccctgctcatcttgcttcaatagcagctttctac-tatcta-aatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
      ||| ||  |||  |  |         ||       ||||  |  |||||  |||  ||| || ||||     || |||    || ||||||||     |||||||||||||  ||||||| |||||||| ||||||| |||||||||||| |||||||||||||| ||| ||||||| ||||||||||||||  |||| |
aaggaatttgtcaagttaatgctgattttgcacttcctactcttccttttcagctaactatgtatttagaattctctgtttactcacatt-tcatcttc-----agATTGCTCGTATATTGACTGTGAAAAGAGAGCGGGAAACTGAACAAGGAATAAACAAGAGATTGTCCAGGGAGCTTGATAGGAAATGGAAGCAGGGCATTG

upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G028216_T01 (Zea mays), 3'ss of exon 1
------tttttttcctgttgtttttctcaccctgctcatcttgcttcaatagc-agctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
      || |     |  || |  | |  | || | ||  || | |    ||  | |  | ||   |   ||||     || |||    || | ||||||     |||||||||||||||| || || |||||||| ||||||||||||||||||||||| || |||||||||||||||||||| |||||||||||||| ||||| |
aggaatttgtcaagttaatgctgattttgcacttcccacttttcctttccagttaaccatgtat--ttagaattctctgttcactcacatttttatcttc-----agATTGCTCGTATGCTAACCGTGAAAAGAGAGCGGGAAATTGAACAAGGAATCAATAAAAGATTGTCTAGGAAGCTTGATAGGAAATGGAAGCAGAGCATTG

upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G14350.1 (Glycine max), 3'ss of exon 1
tttttttcctgttgtttttctcaccctgctca---tcttgcttcaatagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
      |   ||   | |    |  ||||  |     |||| |  || |   || | |    | |    | |    | |  ||  |    || | |  | ||||||||||| ||||| ||||| ||  | ||| | ||||||||  | || ||||| ||||| |||||||| |||||||| |  ||||||||| ||||||| |
--caaataaggtcagtctctggagtctgcataatgctttgcatttattgtctctatgttactttttgggtgaatgataatgtgactgcaaatatccata-cagATTGCTCGCATGCTTACTGTGAAGCGGGAAAGAGAAATTGAGGAGGGTATCAATAAGAGGTTGTCTAGAAAGCTTGATAAAAAATGGAAGAAAAGCATTG

upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv12s0121g00010.t01 (Vitis vinifera), 3'ss of exon 1
tttttttcctgttgtttttctcacc-ctgctcatcttgcttca-atagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
  |   |     ||||||  |      |||| |   ||  | |     |      ||   || |   |     ||||| ||      |    |    |  || ||||||| ||||| ||||||||| | ||| |||| || ||  | |||||||||||||| ||||| || ||||| ||| || | |||||| ||||||| |
--tgagtatgagtgttttggtgggggttgctgaaaatgacttatgcctcgataacctttgattttggtagcatattgatttaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG

upper sequence: LOC_Os02g51790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv07s0141g00200.t01 (Vitis vinifera), 3'ss of exon 1
--------tttttttcctgttgtttttctcaccctgctcatcttgcttcaatagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
         | ||||  ||  | ||     |     || ||   || || ||  |    ||  |   | |    | |   |||| |       |    |    |  || ||||||| ||||| ||||||||| | ||| |||| || ||  | |||||||||||||| ||||| || ||||| ||| || | |||||| ||||||| |
gaggataagtgttttggtgggggttgctgaatatgacttat---gcctcgatgac---ctttgat--tttggtatcatatttgattcaaagcttttcttcaataatagGTTGCTCGCATGCTCACTGTCAAACGGGAAAGGGAGATCGAGGAGGGAATCAACAAGAGGTTGTCAAGAAAGCTCGACCGGCAGTGGAAGAAAAGCATTG

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|88998281|gb|CI038166.1|CI038166
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCGAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|86848837|gb|CI295672.1|CI295672
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACT
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACT
EST: gi|86534146|gb|CI174352.1|CI174352
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88976407|gb|CI024620.1|CI024620
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|86423018|gb|CI060591.1|CI060591
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|13165269|gb|AU174066.1|AU174066
EST:     CCGNGCGCCAGGAGTTCAAATCCAGCAAGTTCGGCCGNATGCGCAAGANG                         ATTGCTCGTATGCTGACTGT
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGT
EST: gi|86829300|gb|CI284965.1|CI284965
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88486097|gb|CI423368.1|CI423368
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|86250583|gb|CI003701.1|CI003701
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|86415488|gb|CI029499.1|CI029499
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88989005|gb|CI040732.1|CI040732
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|33801814|gb|CF326780.1|CF326780
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88963875|gb|CI031208.1|CI031208
EST:     CCGCGCGCCAGGAGTTCGAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88832443|gb|CI019384.1|CI019384
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|86418572|gb|CI032781.1|CI032781
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88507695|gb|CI435201.1|CI435201
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
EST: gi|88982655|gb|CI028068.1|CI028068
EST:     CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGG                         ATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC
genomic: CCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATC

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), 74 (downstream exon)
Score: 33

GGAAGTGGTGGACCTGAAGGGGGAGCTCTTCATGCTCCGCCTCAAGCGCTCCGCGCGCCAGGAGTTCAAATCCAGCGAGTTCGGCCGCATGCGCAAGAGGgtatgtctct ... ttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG
                         cattgac  putative branch site (score: 33)
                                        tcatcttc  putative PPT
         tactatctaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttcctgttgtttttctcaccctgctcatcttgcttcaatagcagctttctactatctaaatttagcattgacttgggttgtcatcttcgcatcagATTGCTCGTATGCTGACTGTCAAAAGAGAACGGGAAATTGAACAAGGAATCAACAAGAGATTGTCTAGGAAGCTTGACAGGAAATGGAAGCAAAGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - ctgttgt
- - - - - - - - - - - - cctgctc
- - - - - - - - - - - - - - - - - ttgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg