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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaggactacacattttgagaatatctaattccgtttacaaggatttgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC

Basic information

species Arabidopsis thaliana
transcript AT5G11700.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 16
gtaacaggactacacattttgagaatatctaattccgtttacaaggatt--tgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
   |   || || |  ||   | || ||        |  |   | | ||  |  || ||| | | || | ||  | || |   ||  |  | | | |    |||||  |||||||  | ||| | ||||| |  ||| | |||||||||||||| || |||||||||||| | || ||||||||||| |||| |||||||||||
-agaattgattatatcttggaataaaattattaaatgaatgtcatgtttgatagtgttgtgatgcttggaattaacatctgcctacttcataaatctt---tagGTGACTGCAACTCCTGATCTTATGCTGGGCTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGCCAAAGGTTTC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 14
gtaacaggactacacattttgagaatatc-taattccgtttacaaggatttgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
 ||  || || | | | |       |||  | | |   | |||||  ||  ||     | |  |   | ||  |  |||   |     |||    |   |||||| ||||| ||  | ||||| ||||| |  ||| | |||||||| ||||||||||||||||||||| | ||||| || ||||| ||||| |||||||| |
-tacaagaaccaga-actgcacttgtattatgaatttttatacaattatcagtct-catcacatcatggattgaggtatgctttctggttttccatttgatagGTTGCTGCTACACCAGATTTAATGCTGGGTTATTTAGATTTCTTTCTTGGTGGGGATGAAAAAAGGCCTGACCTCCCCCCTCGTCTTCATCAAAGGTTGC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G350818_T01 (Zea mays), 3'ss of exon 9
gtaacaggactacacattttgagaatatctaattccgtttacaaggatttgttggtgtaaggtttagt-atatatat-atatatatatatttatttt--aat--atagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
     || |    | |   |  |    |    || |  || |||   |||   |||| |  || | || |||||||  ||  ||   |  | ||||   |||  |||||| ||||| ||  | ||||| ||||| |  ||| | ||||||||||||||||||||||| |||||||| || ||||| ||||| ||||| ||||||||||
----tagtatcggaaagcatagg----ttgcgttactcttgcaattgtttacaggtgaattgtcttgtcatatataggattgatggtttctgatttccaaattaatagGTAGCTGCTACTCCAGATTTAATGCTGGGTTATTTAGATTTCTTCCTTGGTGGGGATGAGAAAAGGACTGATCTTCCTCCTCGGCTTCATCAAAGGTTTC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM5G820781_T01 (Zea mays), 3'ss of exon 1
gtaacaggactac-acattttgagaatatctaattccgtttacaaggatt---tgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
      || | |    ||  ||   || |  | |   |||| ||| |||    | ||    |   |  ||  || ||| |  || | |   |||    |  | |||||  |||||||| | ||||| ||||| | |||| | |||||||||||||| || |||||||| ||| | || ||||||||||| ||||  ||||||||||
----ttggtcaattgtatactgtttatgttcattcttgtttccaaagatggaatattatcttccagcctatcatttatttg-atttctgcttttgcaatc-tctagGTGACTGCAACCCCAGATTTAATGCTAGGGTATTTAGATTTCTTCCTTGGGGGAGATGAAAAGAGGCCTGATCTTCCACCTCGTCTTCGTCAAAGGTTTC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 6
gtaacaggactacacattttgagaatatctaattccgtttacaaggatttgttggtg---taaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
 |      |||  | | | |    ||    | |   |||| | | | |    | ||    |   |  |   || ||| || || | |   |||    |  | |||||  |||||||| | ||| | ||||| | |||| | |||||||||||||| || |||||||||||| | || ||||||||||| ||||  ||||||||||
-ttgatcaactgtatactgttt--atgctcattattgtttccgaagctggaatagtacctttcagcctgtcatttattta-atttctgcttttgcaatg-tctagGTGACTGCAACCCCAGATCTAATGCTAGGGTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGTCAAAGGTTTC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 16
gtaacaggactacaca-ttttgagaatatctaattccgtttacaaggatttgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
 ||| |   ||   ||  ||  |   |||  || || |   | ||| ||||  |  |  | | | |   ||| || | || ||  |  | ||   ||||||||||   |||||| || ||||||||||| || ||| |||| ||||| ||||||||||||||||| |||| ||||||||| |||||| | ||  ||||||| |
ataagatagcttttcaacttctaatttattgaaatctgaacagaagtatttaatatta-atgctatgtcata-atgttta-attgacctgtaaaataatatagGTAAATGCAACTTCTGATTTGATGCTGGCATATATGGACTTCTTTCTTGGTGGGGATGAAAAGAGGATAGACCTTCCTCCTCGATTACATGAAAGGTTCC

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA06G09360.1 (Glycine max), 3'ss of exon 16
-------------------gtaacaggactacacattttgaga------atatctaattccgtttacaaggatttgtt--ggtgtaaggtttagtat-------atatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
                    |       ||    |  |||| |      | ||  ||||   ||| |  |  || |||  |||| |    ||  | |       || |  ||  || |   | ||   ||| ||||||   |||||| || || |||||||| || ||| |||| ||||| ||||||||||||||||| || | ||||||||| |||||| | ||  ||||||| |
gtttgacttgttcttgtacttgttgaacctgtgaacattgaaatatttgacattcaattg-attttcttgtgttggtttaggtgcagctcttgatcttgttctaatttgcattcatcttgttctaaaataaaatagGTAAATGCAACTTCTGACTTGATGCTGGCATATGTGGACTTCTTTCTTGGTGGGGATGAAAAGAGAATAGACCTTCCTCCTCGATTGCATGAAAGGTTCC

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|86068464|gb|DR364221.1|DR364221
EST:     TCCTGTTTACGCTCCTGTCGCTCCCGAGCTTTTATACGAGGGGTCTGAAG                         GTCGCTGCAACCTCCGATT
genomic: TCCTGTTTACGCTCCTGTCGCTCCCGAGCTTT-ATACGAGGG-TCTGAAGgtaacaggac ... tttaatatagGTCGCTGCAACCTCCGATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttggtgtaaggtttagtatatatatatatatatatatttattttaatatagGTCGCTGCAACCTCCGATTTGATGCTTGCGTATCTGGATTTCTTCCTTGGTGGGGATGAAAAAAGGACAGACCTTCCACCTCGACTTCACCAAAGGTTTC
                                            ttttaat  putative branch site (score: 3)
                                        tttatttt  CT-rich tract
               tttagtatatatatat  TA-rich tract