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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggcctgtttgcaaacagaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 10
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggcctgtttgcaaacagaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag
||||||  | ||||| ||||||||| |||| |||||||||||||| |||||||| || ||||| ||||| || ||||| || || |||||||| ||||| || |||||| ||||||    | |||||  |  |||  | ||   |  ||  ||| |     |  |   ||||   | ||||
AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggtctgtttcagcatagaataaaataatttagcaagca--cttgtctaacagtttttt---tttttcaaatcag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 9
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggcctgtttgcaaacagaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag
||||||| | ||||| ||||||||| |||| |||||||||||||| |||||||| || ||||| ||||| || || || || || |||||||||||||||||  || || || |||    | | |||  |  |||  | || || |  | |   | |||         ||||   | ||||
AGTACCTATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATTAAGACAGTCGGTGCAGGCTTTGAGgtatgtcggtctatttcagcataaaattaaataatttagca-agcacttaacagcttgc--------attttgcaaatcag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 10
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggcctgtttgcaaacagaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag------------------------
|||||||||||| |||||||| | |||||| ||||| |||||| | || ||||| || || |||||||| || || |||| ||| || ||||   | |||||   | |||    ||    |     | |       ||   | ||    ||  |  |    | || | | || ||| | ||                        
AGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAGCATAATGAAATTCAGACTGTCAATATAAAAAGTGTAGGAGCAGATGTAGAGgt--atgggctctattattcatttttttggctgtataatttgcgagcaagaagtgttaagtt-ctctttatttttagtgagatgtgtaagtactatgcttcttag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 10
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcag---------ttggcctgtttgcaaacagaatcgatca-atcaaa---cagagaagctgatctcatgccctactatgttttcttattcag---------
||| ||||||||||| ||||| | |||||||||||| || ||||| || ||||| || || ||||||||||| || || | ||| || ||||  ||||||||  |         |  || | ||  ||    |  |  || | ||  ||    |    ||     || | |    ||  |  ||||||     |         
AGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAGCATAATGAAATTCAGACTGTGAATATAAAGAGTGTGGGAGCAGATTTTGAGgtttgaacttaaattcagcttattctcattttggttacatgacattgaagcttaagtgagaaatccttaaggttcacatttctttcttgccatgccttctcag

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 5'ss of exon 10
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgt---cagttggcct------gtttgcaaaca-gaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag----------------------
 | |||||| ||||||||||||| ||||||||| || || ||||| || || || || ||||||||||| || || ||| | ||    ||||  ||||||||   || |  |         | | || |    |  | | ||      |   |||| |     | | | | |   || |   |   || |                       
GGAACCTGTTGCAAGCATGGATAACAGTGGAAAGATTATCTGGGCCAAGCAGAATGAAATACAGACTGTAAATATTAAAGCAGTCCCAGCAGATTTTGAGgtattcactaagttccgagtggctagctattgtgggttggtcgtcatgaacaagaatccttattgaagtcgttgaatatgggcacttttaagagcttgcatctggtttcacag

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|58609972|gb|CK038005.1|CK038005
EST:     ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAG                         GTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT
genomic: ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggc ... tcttattcagGTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT
EST: gi|29630380|gb|CB635389.1|CB635389
EST:     ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAG                         GTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT
genomic: ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggc ... tcttattcagGTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT
EST: gi|58685771|gb|CK074458.1|CK074458
EST:     ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAG                         GTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT
genomic: ATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggc ... tcttattcagGTTACAGATGGGGAAAGATTGCCATTGGCTGTTAAAGAATTAGGAAGTTGT