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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG

Basic information

species Oryza sativa
transcript LOC_Os12g03470.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 17
gtaccagtttagttgacattatttccgcccttcattttcttatcactccc-taatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                                   |     |||| |  |    |   ||| |  || |   ||||  |  |      | |   | ||||||| || |  | |||||||||||||||| | || ||||||||||||||||| || |||||||
----------------------------------gtacaagatcaattacactgtttcatactctctcttttttctcatcatcacctaattatcacatttgaaatccatgtaaaagCTTTCTGAGGACATAGGTGCTGCCCCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 8
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                          |  |    || |  |    ||     | | |   || ||| |   |    |   |      ||| ||   | |||| ||||||||||||||| | |||||||||||  |||  ||||||||||| || |||||||
--------------------------gtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaa--ctctgaaatctacatcaaagCTTGCGGAGGACCTGGGTACTGAACCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 8
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaat-ttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                 || | ||||  |    |     ||| |||| | | |   ||| ||   |||   | ||||  |     |  | | |  || ||||| ||||| ||||||||| | ||||||||||| ||||||||||| ||||| || |||||||
--------------attatgagttccttcaggtaccagttta-cactgcttcactttat-ttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 8
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                                 |     ||| |||| | | |   ||| ||   |||   | ||||  |     ||||  |  |  ||||| ||||| ||||||||| | ||||||||||| ||||||||||||||||| || |||||||
-------------------------------gtaccagttta-cactgcttcactttat-ttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATCTGGGTATTCAACAATG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 8
gtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaat-ttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                                 |     ||| |||| | | |   ||| ||   |||   | ||||  |     |  | | |  || ||||| ||||| ||||||||| | ||||||||||| ||||||||||| ||||| || |||||||
-------------------------------gtaccagttta-cactgcttcactttat-ttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaagCTTGCGGAGGACCTGGGTGCTGCCCCAATATGGGTATTCAACAATG

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|29667817|gb|CB664092.1|CB664092
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAG                         CTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagttt ... tacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
EST: gi|55410431|gb|CV722807.1|CV722807
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAG                         CTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagttt ... tacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
EST: gi|29630007|gb|CB635016.1|CB635016
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAG                         CTTTCTGAGGACCTGGGCGCTGCCCCAATTTGGGTGTTTAACAATG
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagttt ... tacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
EST: gi|33675310|gb|CF303549.1|CF303549
EST:     TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAG                         CTTTCTGAGGACCT
genomic: TTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagttt ... tacatcaaagCTTTCTGAGGACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaagCTTTCTGAGGACCTGGGCGCTGCCCCAATCTGGGTGTTTAACAATG
                       ttctaat  putative branch site (score: 2)
     tttgaattctattttt  TA-rich tract