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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcctaccactgttagctttcgttgccaagttgtaattatttgggtttcgtttgatttgtttttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG

Basic information

species Arabidopsis thaliana
transcript AT2G46230.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 3
--------------------------------------------gtaagcttcctaccactgttagctttcgttgccaagttgtaattatttgggtttcgttt--gatttgtttttggat----cagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG
                                                 ||  | || | || ||| ||              |   | ||| |||||  | |  | ||||  |||| ||    ||| || | |  | || |||  |||||||||   |||||  || || |||  || ||||| |||||||||||||| || ||||||||||| ||||| ||||||
gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgtattattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 3
--------------------gtaagcttcctaccactgttagctttcgttgccaagtt--gtaattatttgggtttcg---tttgatttgtttttggat----cagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG
                     |   |  | |   | ||   |  ||  ||||         |  || ||| |||||     |||| ||||  |||| ||    ||| || | |  | || ||| ||||||||||   |||||| || || |||  || ||||| |||||||||||||| || ||||||||||| ||||| ||||| 
gtaagcttccatcctcactctttccccccttctaattgactgagtttattgcttttcccccttgttcttttggttttaatctttggtttggatttgtattattcagTCCAACTCATTCTTCAGCGCTTTTCTTTCAATACAACACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAA

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 1
-------------------------------------------gtaagcttcctaccactgttagctttcgttgccaagttgtaattatttgggtttcgtttgatttgtttttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCT-TACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG
                                           || |   |  |        ||  |||  ||      |||   ||| |    ||| |||||| ||    ||   | || || |||  | |  | |  ||||| |||||  |||||  || ||||||  || ||||||||| ||||||||||||| ||||||||||| || || ||||| 
gtaagccttcattctctccattttacttttcttctgtttccttgtgaatatattgttttccctatttttaatttattttttggttttaataatcttttgtttgaatttgcattat-ttagTCCAAGTCATTCATCGGCACTTTTTTTTTCAATACAATACTGCATTGGGACCCCCTTACCGTATTTTGGTGGATACCAACTTCATCAATTTTTCCATCCA-

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|86051132|gb|DR346887.1|DR346887
EST:     GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGT                         ACCGAGTGTTCCT-CAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
genomic: GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
EST: gi|86051135|gb|DR346890.1|DR346890
EST:     GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGT                         ACCGAGTGTTCCT-CAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
genomic: GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
EST: gi|86051133|gb|DR346888.1|DR346888
EST:     GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGT                         ACCGAGTGTTCCT-CAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
genomic: GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
EST: gi|164232504|gb|ES192846.1|ES192846
EST:     CCGAGAAACGT                         ACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
genomic: CCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
EST: gi|86051134|gb|DR346889.1|DR346889
EST:     GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGT                         ACCGAGTGTTCCT-CAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
genomic: GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCC
EST: gi|164231305|gb|ES158777.1|ES158777
EST:     GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGT                         ACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATT
genomic: GAGGTTCTGAATCCAAACAAGAAGGACCTCACGGAACTTCCGAGAAACGTgtaagcttcc ... tttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgttgccaagttgtaattatttgggtttcgtttgatttgtttttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG
                                 gtttgat  putative branch site (score: 5)
                                       tttgttttt  CT-rich tract
           aagttgtaattattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcctaccactgttagctttcgttgccaagttgtaattatttgggtttcgtttgatttgtttttggatcagACCGAGTGTTCCTGCAGGGCTTTTCTTTTCTTACAACTCTACATTGGTTCCTCCTTACCGTGTTTTGGTGGATACTAACTTCATCAACTTCTCTATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA