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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagtaaactgagttttggagacttatgttgaacgtagctgtgcttcatctgactcggttctttacggtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC

Basic information

species Oryza sativa
transcript LOC_Os01g07310.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 6
gtaagcagtaaactgagttttggaga-cttatgttgaacgtagctgt-gcttcatctgact-cggttct----ttacggtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC
||||||| || ||   | ||||| ||  ||  ||| |  || | | | ||| |||||||    || |||    ||   |  ||||||||||||||| |||||||| ||| |||| |||||||| |||||||||||||||||||| ||||||||||| || ||||||||||| |||||||| |||||||
gtaagcattagaccaggctttggggagtttgcgttaactgtcgatatcgctccatctgatcatgggtctgcatttgttgcctctgcagTTTTTCATCGTGCTGTCGTGCCTGATTTCAGTCTCGGTGAACTTCAGCACTTTTCTCGTGATCGGGAAGACGTCTCCTGTAACCTACCAAGTCCTTGGCC

upper sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081848_T03 (Zea mays), 3'ss of exon 6
gtaagcagt---aaactgagttttggaga---cttatgtt---------gaacgtagctgtgcttcatctgact-cggttct----ttacggtatctgca----gTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC
||||||| |   || |   | || || |    ||||||||         ||  |||  |    |||||||||   ||| |||    |||| || ||||||    ||| ||||| |||||||| ||| |||| || ||||| || |||||||||||||| |||||||||||||| || || |||||||| |||||||| || ||||
gtaagcattgttaatccaggcttcggggggagcttatgttttagctgtcgatagtactttcatttcatctgatcacgggtctacacttactgtctctgcatgcagTTCTTCATCGTGCTGTCGTGCCTGATCTCGGTCTCGGTAAACTTCAGCACTTTCCTTGTGATCGGGAAGACGTCGCCTGTAACCTACCAAGTTCTCGGCC

upper sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------gtaagcagtaaactgagttttggagacttatgttgaacgtagctgtgcttcatctgactcggttctt-tacggtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC
                    |     |  ||||| | |    ||   |  || |   | |  |  | || ||| | |    || ||| |  | |   ||||||| ||||| || ||||| ||| | ||||||||||| || ||||||||||| |||||||| || || ||||| |||||||| || || || || || || |
gtgagactcaatttcccggggattctaccaaacttattaactgatcttcttgcttc-catgtcgatcctgcatattaacgagtgcttctttgttgattgcagTTCTTCATCGTCCTGTCTTGCCTCATATCAGTCTCTGTAAACTTCAGCACATTTCTTGTCATTGGAAAAACATCTCCTGTCACATATCAGGTTCTAGGAC

upper sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcagtaaactgagttttggagacttatgttgaacgtagctgtgcttcatctgactcggttctttacggtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC
|| |||| | ||        |     ||| | |       |    |  |   ||  |     |||| | |      ||||| |||||||||| || || |||||||| || |||||||| || || ||||| ||||||||||| || || || || || || || || || || || || |
gtgagcatttaaagatccactaaccgcttttttcttcttcatgaattttcggtcccatcttattctgtgca----ttgcagGTTTTCATTGTTCTATCCTGCTTGATCTCTGTCTCAGTCAATTTTAGCACCTTTCTTGTGATTGGCAAGACATCGCCCGTCACCTATCAGGTCCTGGGGC

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|157650172|gb|EX449806.1|EX449806
EST:     TTTTGACTAACCAAAATGTCTTTGCTTTTGATTACACATCTCAAGTTGTG                         TTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCGGCACT
genomic: TTTTGACTAACCAAAATGTCTTTGCTTTTGATTACACATCTCAAGTTGTGgtaagcagta ... gtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACT
EST: gi|29663299|gb|CB659574.1|CB659574
EST:     TTTTGACTAACCAAAATGTCTTTGCTTTTGATTACACATCTCAAGTTGTG                         TTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACT
genomic: TTTTGACTAACCAAAATGTCTTTGCTTTTGATTACACATCTCAAGTTGTGgtaagcagta ... gtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgttgaacgtagctgtgcttcatctgactcggttctttacggtatctgcagTTTTTCATTGTGCTGTCATGCTTGATATCAGTCTCAGTGAACTTCAGCACTTTTCTTGTGATCGGGAAAACCTCTCCTGTAACTTACCAAGTGCTTGGCC
                         atctgac  putative branch site (score: 3)
                                    ttcttta  TA-rich tract