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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt------tgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
|| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |         || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||    ||
gtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatat------ctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
|||| | || |||||||     || | | ||||| ||   |  |||||| | |||  |||| ||| ||||       |   || ||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||  ||||
gtaaagtcttgagcctg-----tggttattggttgatgagtcaaaacatatgttacatagtgaatcatatgatattttccttttcagATTGGCTGGATCTATGGATCAGTTACAGAGGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGCCTG

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 12
gtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt------tgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG----------------------
|| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |         || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||||    ||                      
gtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcagattggctggatctatggatcagTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTGCATTCAAAGGTTCTGCACCTCT

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
----------gtaaggactggagcctg-attgctgttaactggttaattgattg---------aaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
           |  | | ||   |||| |  | |  |  ||   || |||||           | | |||||  |||||  |   | |  ||||  | ||| | || |||||||| ||||| ||||||||||||||  | || |||||||| ||||| |||||||| ||||| || || |||||||| ||| |    || |
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcat-tgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG

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|29632757|gb|CB637766.1|CB637766
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACATACTGGGGGAAAGAG                         ATTGGCTGGATCTACTGATCAGCTACAGAAGATATTCTAACTGGT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGT
EST: gi|15008337|gb|AU222725.1|AU222725
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|58607492|gb|CK035525.1|CK035525
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTAAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86882518|gb|CI327259.1|CI327259
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGG-AAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAT
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|163928491|gb|EG711376.1|EG711376
EST:     CAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: CAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29675228|gb|CB671503.1|CB671503
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|29628005|gb|CB633016.1|CB633016
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
EST: gi|86876412|gb|CI318407.1|CI318407
EST:     TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAG                         ATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG
genomic: TTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactg ... tttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactggttaattgattgaaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG
                                           tctttgtt  CT-rich tract
                 aaacatttcttaacta  TA-rich tract