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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggttgccactttatggtctaatacattgattacattctcatgacttgtgagtttgatggtttttgtgccatgtactgatatattcttctactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCGACATGTTCAAAGGCTCAATGAGGCTTGCGGTGGACAAGTGGGGGCGTAT

Basic information

species Oryza sativa
transcript LOC_Os01g13700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G067522_T01 (Zea mays), 3'ss of exon 1
tgggttgccactttatggtctaatacattgattacattctcatgacttgtgagtttgatggtttttgtgccatgtact---gatatattcttctactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCGACATGTTCAAAGGCTCAATGAGGCTTGCGGTGGACAAGTGGGGGCGTAT
||| ||  |  |||||  | | ||    ||   || |  |  |   |  |   |||||  ||   | || | ||  ||   ||| |  |||||| || ||||||||||||| |||||||   ||| ||||||||| |||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||| ||
tggctt--ctttttatc-tttgatgtcatgtggacgtcatggttgatgattgttttgactgtgcatttgtcctgggcttatgatgtgctcttctcctttgcagTTGACTTGCTGAAGCCCAATGCGACAGTGATCTTGCGCAATGCCAAAATAGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAGTGGGGGCGGAT
















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|86510162|gb|CI152795.1|CI152795
EST:     CATCGGCGACGAGACCGGCGCGATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGTTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|86433411|gb|CI093754.1|CI093754
EST:     CATCGGCGACGAGACCGGCGCNATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|86416330|gb|CI030341.1|CI030341
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCGATGCCGAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|88203281|gb|CI203130.1|CI203130
EST:     GACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: GACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|89198888|gb|CI252962.1|CI252962
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|89167311|gb|CI252842.1|CI252842
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|88212009|gb|CI211649.1|CI211649
EST:     CATCGGCGACGAGACCGGCGCNATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|86253927|gb|CI058654.1|CI058654
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|86422122|gb|CI059695.1|CI059695
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|87026342|gb|CI280253.1|CI280253
EST:     GGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: GGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|86424246|gb|CI063007.1|CI063007
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCGAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|88209624|gb|CI209473.1|CI209473
EST:     GGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: GGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
EST: gi|88200037|gb|CI199887.1|CI199887
EST:     CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAG                         TTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG
genomic: CATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCG

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: 61 (upstream exon), 75 (downstream exon)
Score: 40

CGGCCGGGCGTCGCCGCCCCGTCCCGCCCCCCGCGCATCGCGGAGTGCCTCATCGGCGACGAGACCGGCGCCATCGTCTTCACCGCCCGCAACGAGCAAGgtgggtgagg ... tactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCGACATGTTCAAAGGCTCAATGAGGCTTGCGGTGGACAAGTGGGGGCGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgagtttgatggtttttgtgccatgtactgatatattcttctactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCGACATGTTCAAAGGCTCAATGAGGCTTGCGGTGGACAAGTGGGGGCGTAT
                             tactgat  putative branch site (score: 40)
                                       ttcttctact  putative PPT
                                  atatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggttgccactttatggtctaatacattgattacattctcatgacttgtgagtttgatggtttttgtgccatgtactgatatattcttctactatgcagTTGACTTGTTGAAGCCTGGTGCTACAGTGATCATGCGCAATGCCAAAATCGACATGTTCAAAGGCTCAATGAGGCTTGCGGTGGACAAGTGGGGGCGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- -gttgcca
- - - - - - - - - - - - - - - - - cattctc
- - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtac