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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG

Basic information

species Oryza sativa
transcript LOC_Os06g06980.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 4
gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG--------------------------------
                                                                                               |||||| |||||||||||||| ||||||||||||||||| || || |  ||||||||||| || || || ||||||||||||||||| ||||| ||||                                
-----------------------------------------------------------------------------------------------cttggccatggacatcaaccgcgagaactacgagctgggcctgccctgcatcgagaaggccggcgtcgcccacaagatcgacttccgcgagggtcccgcgCTCCCCGTCCTCGACGACCTCATCGCGGAG

upper sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099363_T03 (Zea mays), 3'ss of exon 2
gtcagcaaca---cgcaaatcccccatctct-tccatcgcagatctggcaa-----------gaaatccccaatcgattgacgtccatccctctgctaactaat-----gcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG
||| |   |    | |   | | |  ||||| ||  || |||||||| ||             |    |   | |  |    |||  || ||||| |            |||||||||||| |||||||||||||| |||||||||||||| || || || |  ||| | ||||| || ||||  ||||||||||||||||| ||||| ||||
gtcggtgccctttctctctttctctctctctctctttcccagatctgccacccacccagaccaaggatctttacccctctctgtctctctctctgttgctcgtccccccgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTAGGCCTTCCCTGCATCAACAAGGCCGGCGTGGGCCACAAGATCGACTTCCGCGAGGGCCCCG

upper sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 5
------------------------------------------gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG
                                               |   | || || |  | | |  | |   | | |||    |||| | | | |  ||  |     |   |   ||  |   |    |||||||||||| |||||||||||||| ||||||||||||||||| || || |  ||||||||||| || || || ||||||||||||||||| ||||| ||||
gtccgtcgttgttccctcccttttctcagatctgccaccccacctccctgaaggcgaagcagctagcggtcctcccactgataaaccaaggatttctctctccctc--tctttgttgttcgtcccgccc-cgcagATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGTCCCG

upper sequence: LOC_Os06g06980.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------gtcagcaacacgcaaatcccccatctcttccatcgcagatctggcaagaa----atccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG
                      || |     |   ||||     | ||    ||      ||   | |  |         ||||  ||||||||| |   || |    ||   ||||| |  | ||| ||||||||| |  ||||   || ||  | ||    |||   ||  | |||||||| || || |||||||||||||||||||| ||||| |
gtgaaatctcgtccaagacaactctgtgctccaggaatcattt-tgtccagaatgttcagtccaacgaagacgatgggttcaatt-attgacgtcgagaacttt--cgac-ggtgcagGTGATTGCGCTGGACATCAGCAAGGAGTGGTATGACATTGGAGCGCCGGTAATTCAAAAGGCGGGCGTTGCTCACAAGATCGACTTCCGGGACGGACCTG

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|86822770|gb|CI251837.1|CI251837
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACG                         ATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaaca ... actaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG
EST: gi|29657324|gb|CB653599.1|CB653599
EST:     CCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACG                         ATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG
genomic: CCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaaca ... actaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG
EST: gi|13895951|gb|AU182287.1|AU182287
EST:     CCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACG                         ATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG
genomic: CCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaaca ... actaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCG

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: 70 (upstream exon), 75 (downstream exon)
Score: 51

GCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCCCTCGCCATCCCCGACGACGGCACGgtcagcaaca ... actaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctggcaagaaatccccaatcgattgacgtccatccctctgctaactaatgcagATCTTGGCGATGGACATCAACCGGGAGAACTACGAGCTGGGGCTCCCGTCGATCGAGAAGGCGGGAGTGGCGCACAAGATCGACTTCCGGGAGGGACCCG
                                           taactaat  TA-rich tract