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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactattttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA

Basic information

species Oryza sativa
transcript LOC_Os01g04920.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G477503_T01 (Zea mays), 3'ss of exon 4
---ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactattttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
        | ||  | | || | ||     |   ||||| ||     | |   |  | ||     | |||||      || |  |   || ||   | ||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||
gtaagttgactatgaactttattgcaccaagttttactgcaa-----acagacagaagttcagatttttcattgccattgaatcatatttctttttcttgcagATACATACCTAGATATACATTTAGCTGGCTTGTGGAGCCAATGTGGCAAGTCATAA

upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G14200.1 (Glycine max), 3'ss of exon 5
ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactat---tttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
 || || |  ||   | | |  |  |  || || | | |    | | ||  ||     ||  | | | |  |  | |  ||  | || ||  |     | |||||||||||||||||| || ||||||||||| ||  | || ||||||   |||||||
ctcacatttcaattttctgaatgtatttca-tatttgcaaagctgtctgggcttcagattaaatccactagttcttgtggt--tgatcttaattgtttttcagATACATTCCAAGATACACCTTTAGCTGGCTGGTGCAACCCATGTGGTGGGTCATAA

upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G27840.1 (Glycine max), 3'ss of exon 5
ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactattttgagctattcatca--tagctgta-ctaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
  | || |  ||   | | |  |  |  || || | | |    ||| |      || |||   | ||  ||  |   |||   | || ||  |     | |||||||||||||||||| || ||||||||||| ||  | || ||||||   |||||||
--cacatttcaattttctgaatgtatttca-tatttgcaaagctatgtctggacttctgattaaatccacaagttcttgtggttgatcttaattgttgttcagATACATTCCAAGATACACCTTTAGCTGGCTGGTGCAACCCATGTGGTGGGTCATAA

upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G17680.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactattttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
                                                             |||    || ||   || |     |  || ||  ||  || | |   | || |  |   |   ||  ||      ||  || || || ||    || ||| ||||||||||||||||| ||||||||||| ||  | || ||||||    ||||||
gtaagttttattcaggttacagattctctgaaaatatttaccattttagattgcatgttacttctgtttacaattattctgatatgatgctatgatgtcagaactgcttcaagttatacaaatcatgtatagcttatg-gctgatcttgtttagtctccagGTACATTCCAAGATATACCTTTAGCTGGCTGGTGAAACCCATGTGGTTGATCATAA

upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G42540.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------ttcccagtaaaagccttttagcgggtggcaatactggaagtattatatgaactattttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
                                                             |||    || || | ||||     |  ||  |   |  || | |     |  ||| || |   ||  ||      ||  || || || ||    || ||| ||||||||||||||||| ||||||||||| ||  | || ||||||    ||||||
gtaagttttattcaggttacgatttttctgaaaatatttaccattttagattgcgtgtcacttctacttagaatcattttgatatgatgctgtgaagtcagaactgctcta--tatgttaaatcatgtattgcttatg-gctgatcttgtttagtctccagGTACATTCCAAGATATACCTTTAGCTGGCTGGTGAAACCCATGTGGTTGATCATAA

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|4715717|gb|AU056833.1|AU056833
EST:     AAACTGCTCGGTGTCCCTCTAGTGATGTCCTATCACACCCATGTCCCAGT                         ATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGT
genomic: AAACTGCTCGGTGTCCCTCTAGTGATGTCCTATCACACCCATGTCCCAGTgtaagtaaat ... ccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaactattttgagctattcatcatagctgtactaatgtttttccccctgcagATACATTCCAAGATATACATTTAGCTGGCTTGTAGAGCCAATGTGGCAAGTCATAA
                                tactaat  putative branch site (score: 1)
                                      tgtttttccccctgc  CT-rich tract
                                   taatgttttt  TA-rich tract