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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G23070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                                                            |   | || | || || |  ||||  | |||| ||||  ||| | ||  ||  |||    ||      |  |  |     ||| |  ||  | |    |  ||   |  ||    |||| |  | |||| ||| ||||||||||| |||||||| ||||||||||| ||||| |||||||||||| |||||||||| || |||
gtaaatggttcactttccttcaagtgcaatttttatattatacattgttttggcctggtttttcctttctgagataaaccttaga-atcttgattta--ctgca-tgatataccaatttctccttttgaagtcatacaggtttaa--atctcctcccctgcttgcctcatgc---ttgtgt-ttttactttttacagATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 5
-------------------------gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattcctt---aagttag------ttaagt-------ggtgaatattgtatact-------ctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                         | ||   |||||   |   |||   |   | |||||    || | |   ||     |||||       ||| |  || |   |  |    |||||   |||| |       |||| |         ||  |     || ||        |||  ||| ||||||||||| |||||||| ||||||||||| ||||| |||||||||||| |||||||||| || |||
gtaaatggttcactttccttcaaatgcaatttttttattattacattgtttaggcctggttcttcctttgagataaaccttagaatctttatctacttcatgatagatcaatttctccttttgaagtcatacagatttaaatctcctcccctgcttgcctcatgcttgtgtatttacgttttacagATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
||||    |||||     | || | |  | || | |    ||  | |   || |||     |||  |      |||| || ||     | |  || || | | |    | | || |  ||  | |  | || ||||||||||| || |||||||| ||||||||||| |||||||| ||||||||| | || || ||||| |||
gtaaa---tttaattccaagttcaat--atttcgatggtccttgatt---atcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacag-gtgaattgaagtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctac-tgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
    |     ||  || | | ||  ||   |     ||| || |  |  | | |||    | | |   |   | |  |  |||||  ||||| | ||||   |   ||     ||  || | |   | | || |||||||| || || |||||||| ||||||||||| |||||||| ||||||||  | || || ||||| |||
----gtaacgtatcctcgcagtttatt--ttaacactaatctttcgtt-atttacagttttcccatgatgtgtatctgcgattttttcattc-tgaagtacttctcgtt----atgctgaagagattgcgtggttgcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgaca-gtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgc--------agATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                                 ||      |||| |  | |     |||||   || |||||||   |  |    |  || || |||   |       | || | |    | |  ||||  ||||         |||| ||||||||||||||||| || ||||| |||||||| ||||||||  | ||||| || || |||
---------------------------------gtaaggaatgtattcta-tattttgaattttgcatgtacattcctga-agcccattatcccataatgaaccagcaggttgcaaacctgacaggctaccatttgtttaattgtagATTTTCCGCAAGGAGCCGTTTTTCTATGGTCATGACAATTATGATCAGCTTGTCAAGATCGCTAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttac---cattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                               ||    |  | ||  |    |||| |   ||||    | |||| | |  ||| |     || ||    || |   ||        ||| |  ||  |    ||||   |||| ||||||||||||||||| || |||||||| ||||| ||||||||| | || || ||||| |||
------------------------------gtgaggaagacggtt-tctgttgacgatttttcg--tatgcattgttgccattctgtttacaatcaaccagcttcctatagacctgatagtcgatcattgggtgtt---agATTTTCCGCAAGGAGCCGTTTTTCTATGGCCACGACAATTATGATCAACTTGTGAAGATTGCAAAG

upper sequence: AT2G23070.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcgttttaagctagaatttagttaacttggtttaagctgtaatggaatgacaagaattcgacagtacattttggttattttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                                                                                        | || ||  ||  | | | | ||   |  |  |  | | |   ||  |||||||| ||||| || || ||||||||||||||||||||  | |||||  |||| || ||||| |||
-------------------------------------------------------------------------------------gtgagtctttt-gtctgatcattcgtacttgcta-acgccccaagcttcacagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAG

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|164175472|gb|ES132713.1|ES132713
EST:     GTCTTGGGTGTATGTTTGCTGGAATG                         ATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
genomic: GTCTTGGGTGTATGTTTGCTGGAATGgtaagcgttt ... ctgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
EST: gi|86088019|gb|DR383778.1|DR383778
EST:     ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATG                         ATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
genomic: ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATGgtaagcgttt ... ctgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
EST: gi|47831931|gb|CK121615.1|CK121615
EST:     ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATG                         ATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
genomic: ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATGgtaagcgttt ... ctgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTG
EST: gi|124877321|gb|EH956758.1|EH956758
EST:     ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATG                         ATATTCCGCAAGGAGCCGTTCTTTTATGGCCA
genomic: ATGATTATTCCTTAGACCTATGGAGTCTTGGGTGTATGTTTGCTGGAATGgtaagcgttt ... ctgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccattccttaagttagttaagtggtgaatattgtatactctactgtttgcagATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAG
                                        ctctact  CT-rich tract
                             aatattgtata  TA-rich tract