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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggttttcaatttagcctcacattttctactttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt...

Basic information

species Oryza sativa
transcript LOC_Os01g64780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G149662_T01 (Zea mays), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggtt--ttcaatttagcctcacattttctactttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt
||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||||||| |||| ||||||||||||||||||  | ||   || | ||||  ||  |  | | |  |         ||||      |  |  ||   |   |            |||   |||      
TTTCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAAATTGGAATCGACATATTTGgtaatcattgtacatttagtttaaactttctgtatatggtggttgtaaactaagggaaatgctatactttttcttttcttttgtccttgatgatttttgt--

upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G046098_T02 (Zea mays), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggttttcaatttagcctcacattttctactttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt--
|| |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||| ||| ||||||||||||||  | ||   ||| |    |  || || | ||| | |   ||   || |        |   | || | |     | | |  |  |  | ||| ||   
TTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACATATTTGgtaatccttgta--caaatacttcaaactttctgtacatggtgattgtaaactaatggaaaggctatatttttttcctcttattttatccttgtgatatcct

upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G15360.2 (Glycine max), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggttttcaatttagcctcacatt--ttctactttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt---
||||| |||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||| ||||  | |  || || || ||  | |||||| |  ||  |||    ||| ||||   |||    |  ||||||   |  || ||| | || |    |  |      |   || |  |     | |    |    
TTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATAGATGTGTTTGgtga--gtaattt---gttttgccttcaattaacacagctttgataattatattttccctcctcagaagttacaaatagggattttttattgttctactgtagat

upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggttttcaatttagcctcacattttcta-ctttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt---
||||| |||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||| ||||  | |  || ||||| ||  |||||||| |  ||  |||  |||||  | | |  |     | ||||||   |  || ||| | || |  | |  |      |   || |  |     ||  |   |   
TTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATAGATGTATTTGgtga--gtaattt--aatttgcctttaattaacacagctttgataattatattttccctcctcaaaagttacaaatagggattttttttttgttctactgtata

upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgta---attgtggttttc--aattt--agcctcacattttctactttgaacttcctaattttcttcttgcacacatgtgtgaaaacatgtactgacactttgaaatt
|||||||| ||||| || ||| ||||||| ||||||||||| || || |||||||| || ||||| ||  |||| |  || |||||  | |||||||||||||   ||||   || |    | ||  | | | |  || | ||||  | |   | | || |      | |    |||      || || |  | | |  |       
TTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTTGACATATTTGgtatgaattgaaattcttctgacttgtatcgtaatgttatgtactaagtaaaacttgatgtagaaacttcgtctatgaagtctaagatatcttaatagat-------

upper sequence: LOC_Os01g64780.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 3
TTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtggttttcaatttagcctcacattttctactttgaacttcctaattttcttcttgcacac-atgtgtgaaaacatgtactgacactttgaaatt-------
||||| ||||| || || || ||  | ||||||||||||||||| || |||||||| || ||||| ||| |||||| |   ||||| ||||| ||||||||||     ||||   |||   || |  |  ||  |  || |   |   |  | ||      | |    |   |||| |  |  | |||   |||   | ||       
TTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATCGATATATTTGgta-----ggttcaaaat---gcattgctgttgatctttggttttattttgtctttaggaggtatgggaaaggtgatactaaatgctgcttcttaatatttgtttagt

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|58665417|gb|CK054103.1|CK054103
EST:     TGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTG                         GTCTTGGTTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG
genomic: TGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtgg ... cacactgcagGTCTTGGTTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG
EST: gi|27547116|gb|CA765115.2|CA765115
EST:     TGATGGCTTTTT-AGCCCACTATATGCAAAACTTGGGATCGACATATTTG                         GTCTTGGCTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG
genomic: TGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtgg ... cacactgcagGTCTTGGTTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG
EST: gi|27920852|gb|CB096660.1|CB096660
EST:     TGATGGCTTTTT-AGCCCACTATATGCAAAACTTGGGATCGACATATTTG                         GTCTTGGCTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG
genomic: TGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATCGACATATTTGgtaattgtgg ... cacactgcagGTCTTGGTTTTCTGACTTCTCTGGTATTCATTTTTCTGGTTGGAATATTTG