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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC

Basic information

species Oryza sativa
transcript LOC_Os05g31000.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagcttacgactgctctt----atctagccaatctaaatagttctattagttggattcctg---ttgatgtttg-ctattt------cttttgcccc--atttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
    | ||  |  | |||||    ||  || |||||| |||  |||| ||| |   |   | |   || || ||   || |||      | |||||     |   |||||| | |||||||| || || || ||||| |||||||| ||  |||| ||||| ||||| || ||||| ||||| |||||||||||  ||||||| ||| 
----gtttgtgttttctctttaatattcagtcaatcttaat--ttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaacacagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------gtgagcttacgactgctcttatctagccaatctaaatagttctattag-------ttggattcctgttgatgtt----tgctatttc---ttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
                           ||    |  |  ||         |  || ||||   || | || ||         |||   |||  ||||  ||    ||  || ||   | || |    | ||||||| | |||||||| || ||||| ||||||||||||||||| ||||| || || |||||||||||||||||||| ||||| || ||| ||||||| ||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgat----gtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
                                        | |  ||  | ||  | | | ||    ||| | |    |  |  || ||      || ||||     |||| ||||   ||||       ||||||| || ||||||||||| || || ||||| ||||||||||| || || ||||| ||||| || ||||||||||| ||||| |||||  |||| || || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttatta---ttcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
-------gtgagctt-acgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccattt-cagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
          | ||| |   | | |  ||  ||  |  |  | ||  ||    |    | ||| |  | | |      ||  |   | |  | | || |||||||| ||||| ||||| || || ||||| |||||||||||| |||| ||||| || || || || |||||||| ||||| |||||  |||| || ||  
tataccttcaatctttatcgcagattctacatattct-ttcagatccttgagatgtcagaatttcaatagcttgcaagtaacttcatcgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagcttacgactgctcttatctagccaatctaaat--agtt--ctattagttggattcctgttgatgtttgctatttcttttgcccca----tttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
 | |  | |   |||||   ||   || |   ||  |  ||||  | |  | | |  || |   ||  | ||    |||||||||         |  ||||| |||||||| ||||| || || ||||| |||||||||||| | || |||||| || |||| ||||| |||||||||||||||||  |||| |||||||
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttttgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
                                 |  | |   |  ||| | ||      | ||   |  || |  ||| ||   | || ||||| || ||||| |||||||| || || || |||||||||||  ||||||||||  |  |||| |||||||||||||||||||||||| |||| || ||||
------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaact-tcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: LOC_Os05g31000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
gtgagcttacgactgctcttatctagccaatctaaatagttctattagttggattcctgttgatgtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
                                |||       || ||| || |      | || || |    |  ||  |    | || ||||| || || || |||||||| || || || |||||||||||  ||||||||||  |  |||| |||||||||||||||||||||||| |||| || ||||
-------------------------------gtaagcttgcgtagtagatgaaagagaataga-gtctaacttcgctccttgttctttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|89168944|gb|CI020484.1|CI020484
EST:     AGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: AGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88239218|gb|CI240380.1|CI240380
EST:     AGAAGAGCAAGAAT                         ATCCTTTTCGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: AGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|218484158|gb|FG948739.1|FG948739
EST:     TGAAGTCTATCACTGGTGT-AGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88989765|gb|CI107452.1|CI107452
EST:     TGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88205051|gb|CI204900.1|CI204900
EST:     CCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: CCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88847917|gb|CI006103.1|CI006103
EST:     GTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: GTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
EST: gi|88242439|gb|CI242288.1|CI242288
EST:     TGTTACTGTCAAGAAGAGCAAGAAT                         ATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC
genomic: TGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGAC

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: 74 (upstream exon), 75 (downstream exon)
Score: 154

GCAGAGTCGTAGTGAGAAAAAAAGCAGGAAGGCCATGGTGAAGCTTGGCATGAAGTCTATCACTGGTGTGAGCCGTGTTACTGTCAAGAAGAGCAAGAATgtgagcttac ... cccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctattagttggattcctgttgatgtttgctatttcttttgccccatttcagATCCTTTTTGTCATCTCCAAACCGGATGTCTTCAAGAGCCCTACATCCGACACCTATGTCATTTTTGGCGAGGCCAAGATCGAGGACCTGAGCTCGCAGC
                    tgttgat  putative branch site (score: 154)
                                ctatttcttttgcccc  putative PPT
                                 tatttctttt  TA-rich tract