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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggggattgatttcaatctcatatgcctcatctctcatgttgctgtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA

Basic information

species Oryza sativa
transcript LOC_Os08g44280.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 2
aaggggattgatttcaatctcatatgcctcatctctcatgttgctgtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA
        |    || ||||  |  ||| ||| |||  |||||    |   |    ||   ||     |   ||| |||||| | ||  ||||| |||||||  | |||||||| |||||||| ||||||||||||||| | |||||||||||||| |||||||||||| | |||| ||||| ||| |||||| ||||||
gtcaaccatagagtctatcttgttcgccccatttcttgtgttgagaatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGA

upper sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G423027_T02 (Zea mays), 3'ss of exon 2
aaggggattgatttcaatctcatatgcctcatctctcatgttgctgtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA-----------------
                 |||  |  ||| ||| |||  |||||    |   |    ||   ||     |   ||| |||||| | ||  ||||| |||||||  | |||||||| |||||||| ||||||||||||||| | |||||||||||||| |||||||||||| | |||| ||||| ||| |||||| ||||||                 
-----------------tcttgttcgccccatttcttgtgttgagaatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagcatgggctgtggtccagCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGATGGAGGCCATCGACAGG
















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|88591401|gb|CI707432.1|CI707432
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|58593894|gb|CF992202.1|CF992202
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCGAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|86830372|gb|CI291882.1|CI291882
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|12405082|gb|AU166683.1|AU166683
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|570178|gb|D41027.1|D41027
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGATGGCTAGCGACAAGAACAAGGCAATGGTTGA
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGG-GGCTAGCGACAAGAACAAGGCAATGGTTGA
EST: gi|88377114|gb|CI597898.1|CI597898
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|88359377|gb|CI679904.1|CI679904
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|33817247|gb|CF334460.1|CF334460
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGATGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
EST: gi|33814508|gb|CF333118.1|CF333118
EST:     AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAG                         CACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG
genomic: AAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAG

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), 61 (downstream exon)
Score: 23

CTGCACCGCGACCCACCCGCGCGCTCCCAATCGGCCCCAAGATTAAGATTAAACCAGGAGAGACCACCCGATCGAGTGTTCTCTCACTTTCGCCATGGAGgtactccgct ... actgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA
                                      tgctgat  putative branch site (score: 23)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggggattgatttcaatctcatatgcctcatctctcatgttgctgtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - catatgc
- - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat