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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctgattctcatattattttcttggccatattcatgatgtgcttttcgtctgctttgcttttttttcat...

Basic information

species Arabidopsis thaliana
transcript AT2G38710.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38710.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G24340.1 (Glycine max), 5'ss of exon 2
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctga-ttctcatattattttcttggccatattcatgatgtgcttttcgtctgctttgcttttttttcat-------------------------------------------------
||||| | |||||||||||||| |||||  | || ||||||||||| || |||||||||||| ||||||||| |||  |||| ||||||||  |||| ||||  ||    ||  |     |  |||| |||| | | | |  || ||  || ||||  ||| ||  |||  |  ||||  | |  ||  |  ||   | ||                                                 
AGAAAGTGGTGAATGGTGGAGATCCTCGCCTTCGGGGATGTATTGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTCAAAGATTATGCGCTGACCAGgtttgtttatgttatagggtatcttttattttgtaaatgcaaattttgcttgcttg--cattttgttgaactaatttttatgtcgttcacacttgcattattaaattggtatattccttgtctatgctttgtgcatgcaatatcttgcag

upper sequence: AT2G38710.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 5'ss of exon 2
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctgattctcatattattttcttggccatattcatgatgtgcttttcgtctgctttgcttttttttcat------
||||| ||||||||||||| || ||||| ||||||||||||||||| || || ||||| ||  ||||||||| |||||| ||||| ||||| || || |||||     |  |    |  ||  |  |      | |||  | |||| | |   | ||  |  |  |||  |   | ||  |  |      | |     |       
AGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTTAAGGACTATGCTTTAACCAGgta-----ttattgcaacacatatgctaggcatttatttacttattctatgtcttgctgtggttttga-atctctctctccctccccatctgtcccctacgccaaa

upper sequence: AT2G38710.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S2121_1V6.1 (Physcomitrella patens), 5'ss of exon 1
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctgattctcatat-tattttcttggccatattcat--gatgtgcttttcgtctgctttgcttttttttcat
     ||  |||||||||| ||||| || ||||| || || ||||||||||||||||| ||   | | |||   || ||||| ||||||||  | || ||||| || || || |    |  |  ||   | |   || |  |         || |       || ||   | || ||| |  |    |    ||   |||   
-----ATGTTGAATGGTGGGGAGCCACGCTTGCGGGGGTGCATTGGTACACTGGAAGCCCGATACATTATCTCCGGGTTCAAAGATTATGCACTCACCAGgta-gttctggttccggctgtggattgcgtgttcaatccatactcgcgaactcatactttggtttattaaaagtacttataattccttccagttggcttta--

upper sequence: AT2G38710.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ07623 (Selaginella moellendorffii), 5'ss of exon 2
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttt-tctgattctcatattattttcttggccatattcatg-atgtgcttttcgtctgctt-tgcttttttttcat--------------------------------------------------------------------
||||| | |||||||||||||||||||| ||||| ||||| || || || |||||||| ||| ||||||||| ||||||||||||||| || ||||| |||| ||  ||  |  |   |  |  |        ||  |  |   |  ||||  ||     | |   || |||   |  | |   |||  || ||  |   |                                                                      
AGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTCAAGGATTACGCATTGACCAGgtgcgctcttttggttgcttggcgtgaaagagccttgtcatggcaccatttgtttatggttttaagtggatgccttccttgctagctagtgtttggtagccgagtttcgagcgaaaagatgtgaaaaaaataagtggaaggatgttgacctcttctctacctatgtttcag

upper sequence: AT2G38710.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ11024 (Selaginella moellendorffii), 5'ss of exon 2
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctgattctcatattattttcttggccatattcatgatgtgcttttcgtctgctttgcttttttttcat--------------------------------------------------------------------------
||||| | |||||||||||||||||||| ||||| ||||| || || || |||||||| ||| ||||||||| ||||||||||||||| || ||||| |||| ||  ||  |  |   |  |  |           || ||||   |  || |||   ||  |  | |   | |      ||   | |||  | |||  |                                                                          
AGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTCAAGGATTACGCATTGACCAGgtgcgctcttttggttgcttggcgtgaaagagtc--ttgtcatggcacctt-ttgtttatggttttaagtggatgccttccttgctagctagtgtttggtagccgagtttcgagcgaaaagatgtgaaaaaaataagtggaaggatgttgacctcttctctacctatgtttcag

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|301501251|gb|HO206791.1|HO206791
EST:     CTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAG                         TGCCTTGAGGGATCGCAGGTTCCCACCTATACAGGCCAAAGAATTGCCATC
genomic: CTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactc ... aatattgcagTGCCTTGAGGGATCGCAGGTTCCCACCTATACAGGCCAAAGAATTGCCATC
EST: gi|164181122|gb|ES174439.1|ES174439
EST:     CTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAG                         TGCCTTGAAGGGATCGCAGGTTCCCACCTATACAGGCCAAAGAATT
genomic: CTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactc ... aatattgcagTGCCTTGA-GGGATCGCAGGTTCCCACCTATACAGGCCAAAGAATT
EST: gi|164167137|gb|EL982344.1|EL982344
EST:     GCCTTGACAAG                         TGCCTTGAGGGATCGCAGGTTCCCCACCTATACAGGCCAAAGAATTGCCAT
genomic: GCCTTGACAAGgtacgtactc ... aatattgcagTGCCTTGAGGGATCGCAGGTT-CCCACCTATACAGGCCAAAGAATTGCCAT
EST: gi|125024898|gb|EL097167.1|EL097167
EST:     TGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTCGACAAG                         TGCCTTGAGGGATCGCAG
genomic: TGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTT-GACAAGgtacgtactc ... aatattgcagTGCCTTGAGGGATCGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTCAAGGATTATGCCTTGACAAGgtacgtactcgtcctcattcagttttttttttctgattctcatattattttcttggccatattcatgatgtgcttttcgtctgctttgcttttttttcat

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcattc