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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCGGCATAGGAGTATATAATTCATTTTTGAAGGAAGTTCCATTGAGAAAAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattctgcacatgcttgttttagtaaatgctgccactatattatttgttaaatttaacttaggtattttcag

Basic information

species Oryza sativa
transcript LOC_Os03g58080.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58080.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G073429_T01 (Zea mays), 5'ss of exon 7
GGTCGGCATAGGAGTATATAATTCATTTTTGAAGGAAGTTCCATTGAGAAAAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattctgcacatgcttgtttta-gtaaatgctgccac-tatattatttgttaaa------tttaacttaggtattt--tcag
  | || || ||||| |||||||  ||| ||||||||||||||||||| ||||||||| ||||||| ||| | || |||||||| || |||||||||||||||   |||||  | |     |     ||   | |||| || ||| || |    | ||      ||| |||    |||||  ||||
ACTGGGAATCGGAGTGTATAATTTGTTTCTGAAGGAAGTTCCATTGAGGAAAATCTTTCTTGTGACAACAGTCTTAGGTTCTGCTCTCGGAATGACACAGgtcctcttctgtgcttatagttcccgtgttgttcctgcaacctatgttgtcgaatcaagtttttttttactagcatatttcctcag

upper sequence: LOC_Os03g58080.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G32040.1 (Arabidopsis thaliana), 5'ss of exon 7
GGTCGGCATAGGAGTATATAATTCATTTTTGAAGGAAGTTCCATTGAGAAAAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattctgcacatgcttgttttagtaaatgctgccactatattatttgttaaatttaacttaggtattttcag--------------------
| | ||  ||||| | || |||  |||  |||||   ||||||||||||||||||||| | ||||| ||||| |||||  | |  ||||| ||||| |||||    | | |  |   |||        |||   ||||| | |||||| ||||| |   |||  |    | ||  |                    
GCTTGGAGTAGGACTGTACAATGGATTCCTGAAGACTGTTCCATTGAGAAAAATCTTTCTCGTGACGACAATTTTTGGCACGGGTCTTGGGATGACTCAGgttggttcccgtccgctctttacaagaaaaactttgcca-tctattatctgttacac--aaccaataactcttgggaccgttcttatgttttgcag
















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|29625145|gb|CB630156.1|CB630156
EST:     GGTTCTGCCCTTTGAATGACACAG                         GTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
genomic: GGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
EST: gi|218486530|gb|FG966629.1|FG966629
EST:     AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAG                         GTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
genomic: AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
EST: gi|87006785|gb|CI285819.1|CI285819
EST:     AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAG                         GTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
genomic: AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
EST: gi|58692573|gb|CK081260.1|CK081260
EST:     AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAG                         GTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
genomic: AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
EST: gi|29625062|gb|CB630073.1|CB630073
EST:     AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAG                         GTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG
genomic: AAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGG

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: 51 (upstream exon), 66 (downstream exon)
Score: 8

GGTCGGCATAGGAGTATATAATTCATTTTTGAAGGAAGTTCCATTGAGAAAAATCTTTTTTGTGACTACAATATTTGGTTCTGCCCTTGGAATGACACAGgtcaaattct ... gtattttcagGTTCTTCTTGTCACTGGGCTCAATCGAGTTCTTGGAATCAGTGATGAATGGTTCTCCATTGGTGATTCCTTGATTATCACTGTCCTTGGTCAG




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