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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC

Basic information

species Oryza sativa
transcript LOC_Os05g32110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 4
gtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc---tgcaaaattgctaacaagttccatgcatttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC
||||||| || |        |||||| |||   || | ||| ||  | | ||||    |||||  || ||||  | ||   |||||||   ||| ||| |||||||| || ||||| | || |||||||| ||||| |||||||| || ||||||||||| ||||| ||||||||||||||||| || ||||||
gtgagtttatcag-------ctcttaattcatgtcatattggggttctattttttatttgcaatttttctaatgaatttattgcattttt-cagCGAGGATTCACCTAATCTACAAGCCGCAATTGATGGTCCTGGTAAATGGACTGGCCAGCCTCTTGTACAATGCACTTCTCACATGTGCCCAATAAGAATC

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 4
gtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaacttttc-tgcaaaattgctaa-caagttccatgcatttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC
||||||| ||    |     |||||| |||   || | ||  ||  | | ||||  |  ||| ||  |||   | ||| ||    ||   ||||||| |||||||| || ||||| |||| ||||||||||||||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||| ||||||
gtgagttgatctgccttttgctcttaattcatgtcctattagggttctattttttatctaaagtttttaaatgaattctattgcattttgcagTGAGGATTCACCTAATCTACAAGCTGCAATTGATGGCCCTGGCAAATGGACTGGTCAGCCCCTTGTACAATGCACTTCCCACATGTGCCCGATAAGAATC
















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|29629256|gb|CB634267.1|CB634267
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58662260|gb|CK050940.1|CK050940
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|66918925|gb|CX105773.1|CX105773
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGCAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|66947309|gb|AU312153.1|AU312153
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58686271|gb|CK074958.1|CK074958
EST:     TGCTCTTGTGGCTGCCAAAAGAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58654342|gb|CK043022.1|CK043022
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATCTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|24208701|gb|AU225728.1|AU225728
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|33676440|gb|CF304679.1|CF304679
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|3061251|gb|C91883.1|C91883
EST:     GGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: GGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|24208702|gb|AU225729.1|AU225729
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|58663357|gb|CK052043.1|CK052043
EST:     CAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: CAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
EST: gi|29684532|gb|CB680807.1|CB680807
EST:     TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAA                         TGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC
genomic: TGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGAC

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: 72 (upstream exon), 75 (downstream exon)
Score: 36

GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaat ... atttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgaggcccaacttttctgcaaaattgctaacaagttccatgcatttccacagTGAGAATTCACCTTATTTACAATCTGCCATTGATGGCCCTGGCAAATGGACCGGTCAGCCTCTTGTCCAATGTACTTCTCACATGTGCCCGATCAGAATC
                           tgctaac  putative branch site (score: 36)
                                            catttcc  putative PPT
                      aaaatt  TA-rich tract