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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatttctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g12794.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatt-tctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG
||| |||| | || ||||||  ||     || ||  |   |       |||| |||| || || |  | ||| |||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||| ||||| ||||
gtatgtattgccatgtgggtagcacttctttctcaatagcttga----ttgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G320497_T01 (Zea mays), 3'ss of exon 6
gtaagtatggtcaagtgggtgtcatagtgttttccttgtgtcagcaatttgttgtctaatcttatt-tctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG
||| ||||  ||| ||||    ||     || ||  |   |       |||| |||| || || |  | ||||||||||   || ||| || |||||||||| ||||||||| |||||||| | || | ||| || |||||||||||||||| ||||||||| ||||| |||||||| |
gtatgtattttcatgtggccaacacttccttctcaatagcttga----ttgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG
















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|29656571|gb|CB652846.1|CB652846
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|218486674|gb|FG965210.1|FG965210
EST:     AATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: AATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|4968823|gb|AU065727.1|AU065727
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCT-NTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|88298843|gb|CI566040.1|CI566040
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGGTCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58664712|gb|CK053398.1|CK053398
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58667247|gb|CK055933.1|CK055933
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|87008704|gb|CI302859.1|CI302859
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|218483482|gb|FG958118.1|FG958118
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|9886225|gb|AU102118.1|AU102118
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|218500771|gb|FG968418.1|FG968418
EST:     CCCACGGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: CCCAC-GGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58597071|gb|CK007599.1|CK007599
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58596315|gb|CK006843.1|CK006843
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|4968734|gb|AU065638.1|AU065638
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCT-NTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|4968733|gb|AU065637.1|AU065637
EST:     TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTG                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: TTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC

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), 74 (downstream exon)
Score: 63

CCACATCGAGCAGTGGAATGACTTTTCGGCCACAGAGGTTGATGCTAATATTGGAAAATGGCTCTACCCACGGCTAGGAATTGCTCCCTATGTTGCTGTGgtaagtatgg ... tgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtgttttccttgtgtcagcaatttgttgtctaatcttatttctgcccaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCGGTGACTCTTG
                              gtctaat  putative branch site (score: 63)
                                    tcttatttctgccc  CT-rich tract
                                 taatcttattt  TA-rich tract