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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA

Basic information

species Oryza sativa
transcript LOC_Os01g35050.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 2
catgctcttcatttgtgctac-aatttcctattgtattt----cctttctttttcgaagaaactcttatactccttttca-actgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
       |||   | ||  || |||||     | |||||    |||||| |||         |   |||     | || | | |||   | ||| |   ||| ||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||  ||||||||||||||||||||||||||||||||| || || 
------tttctggtatgtcactaatttgaaggtatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 9
-catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
   ||    ||  |  |  ||| ||  | ||||  |   | ||  ||| ||        | |   | |   |||  | |||   | ||| |   ||| ||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||  ||||||||||||||||||||||||||||||||| || || 
atttgaaggtc-ctgctattaccatggcatatttaagccctttcgtttctccttttgcgtgtatgaatttatttatattgtctatttttcctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
-catgctcttcatttg-tgctacaatttccta---ttgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
  |    | || | ||  | || | |||  ||   |||    |  |   | |  | || |   |   |||  |    | || |  || |||   | | | |||||||| ||||  ||||||||||   ||||||||||||| ||||| || || ||||| ||  ||||||| ||||| ||||||||    |||||||| ||||||
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacc----taaagtaaacatatgc-catgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
           | ||| ||  |      | ||    |  ||   |||  |  ||| | | | |||   ||||   |||       ||| | | | ||||| || ||||  ||||||||||   | |||||||||||||| ||||| |||||||||||  ||||||| ||||| |||||||| || |||||||| || || 
----------gtatgttctttagacctttctt----tgtctgcatttcactgagaga-tatcatat--ctttctgact-------ttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 9
catgctcttcatttgtgctacaatttc-ctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
           |  |||   |  | || || ||    || | |||||||| |   | |  |||    | ||    |    |  || |     ||| |||||||| || | ||| |||||    || || || |||||||||||||| ||||| |||||| ||||||||||||||||||| || || || || || ||| | 
----------gtacgtgactctctatctctgttaatctttcgttctttttgggttacaggctt----ttctaaggactcttctttttaaaaatctgtgcagAATCCCTAAGACTATTGGCATGGCGATACCGATGAAAGCAACCTTCTTTATCACATATATAATGGTTGATGGTTGGGCAGGAGTTGCAGGAGAGATTCTT

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G11960.1 (Arabidopsis thaliana), 3'ss of exon 9
catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
           |  || |     | || |  | | | ||| ||         | | |  |||   ||  | |     || |||    || | |||   || || || | |||  |||| | ||| || || || |||||||| |||||||| |||||| ||||||| || |||||||||||  | || || || ||| | 
----------gtaagttcccttttctctttctctgtctccattggaacagatatagatccttgagcttatgtattgttgcact----tgtcacttgttagGATTCCTAAGACGGTTGGGGTAGCGATACCGATAAAAGCAACGTTTTTTATCACATATATAATGGTGGACGGTTGGGCTGGTATTGCAGGGGAGATTCTG

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctc--tttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
 ||  |       |   |||  |     |    | |||   || | | |     || ||  |  | |  |||   |  ||   |  || | ||  ||| |||||| || || |||||||| | ||||||||||||||||||||| || || ||| | ||  ||||||||||||| ||||||||  |||| |  || ||||||
-ata-taactgcataaactatcaagcttttcgctgttttgattgtatataatctaatcttgtgaaatgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA

upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 8
catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaa-gaaactcttatac--tccttttcaactgtacttatttgcct--ctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
         ||||| || |||    |   |||  || |   |      || |  |  ||| | ||    |   ||| |  |  | | |  ||  |   ||||||| || |||| ||  || ||     ||||||||||||| ||||| || || ||||| ||  ||||||||||||| |||||||| ||  |||| || ||| ||
----aataccatttttgttactggatta-attagatctggatgtgacatcaagtgctactttgatctgatatgtttaatataaagtcaagtggttgattttgcagTATCCCAAAGATCATCGGAACCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTTGATGGATGGGCTGGAGTTTCTGGGGAGATTCTA

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|66923753|gb|CX110601.1|CX110601
EST:     GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGA                         AATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
genomic: GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGAgtatgtcctc ... ctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
EST: gi|87006528|gb|CI294911.1|CI294911
EST:     GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGA                         AATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
genomic: GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGAgtatgtcctc ... ctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
EST: gi|13896907|gb|AU183243.1|AU183243
EST:     GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGA                         AATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
genomic: GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGAgtatgtcctc ... ctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
EST: gi|218495590|gb|FG944779.1|FG944779
EST:     GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGA                         AATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT
genomic: GGATCTGCTTTAGAGCAGCTCAAAACATTTCTTCACCAATCAGCAAATGAgtatgtcctc ... ctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
                                    cttatttgcctcttt  CT-rich tract
                                  tacttattt  TA-rich tract