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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT

Basic information

species Arabidopsis thaliana
transcript AT1G21760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G12130.1 (Glycine max), 3'ss of exon 5
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                                 | ||||  ||   ||||   |||      || |    |     | |  |  ||| ||    ||  | | ||  |     | ||  ||   |  | |||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||| || || ||||| || ||  | 
------------------------------ttcaaattcacgctaaaagtagatgtacatgattttcctattccttttatgttatgtttttagctaggtctctttgtc----ttacagtgctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG

upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G42640.1 (Glycine max), 3'ss of exon 5
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                                 | ||||  ||   |||| | ||       || |    | |   | |  |  ||| ||  ||||  | | ||  |     | || |||   |  | |||||||||||||||||||||| ||||| ||||||||||||||| ||||||||||||| || || ||||| || ||  | 
------------------------------tttaaattcatgctaaaagtaaatgcacatgattttccaattttttttatgttatgtttttatataggtctctttgtc----ttacaatgctcccacatctcagGTCTTTATGTGAGTAGAAATACCTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCTGTACATGTG

upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g02630.t01 (Vitis vinifera), 3'ss of exon 5
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                             |||  | | | | | |   ||||     |   ||  |||  || || || ||| || |  ||   | ||| |  |||  || | || |   | |   | | ||||||||||||||||||||||| || |||||||| |||||| |||| |||||||   |||| |||||||||||  | 
----------------------------ccactcc-tacaatctctgtgtgaa-acctgggttcatat-ttcagattatcattgttttgtgacct-tctgtcctga--aaggaaattcgcttttcacatatcagGTCTTTATGTGAGTAGGAACACCTACATTCGTGCTGGAGTTGCAGAGTGGAGAGTTACCAATCCAGTTCATGTG

upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S96_233V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
    | |     | || | | |||    | |  || || |   ||    | |||   |||  ||  ||  | | | | | |  ||   |     |      | ||  |  |   |   ||||   |  |  ||||  | ||||| || |||||||| ||||||||  ||||||| ||||||||||||||||| |||||||||||  | 
---gtataatggtgttgaccttctg---taaaaacgtttt---gctttataatttagttccatt-cattttttaattca-actgtaattgcacttgggaagagtgtctgtaaggaagttgtactcttgttgcagGATTATATGTAAGCAGGAATACGTACATTCGTACTGGAATAGCTGAGTGGAAGATTACCAATCCAGTTCATTTG

upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ32549 (Selaginella moellendorffii), 3'ss of exon 4
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                                                                                 || | |   ||||    || |    ||  ||| |||     |  |  || ||||| ||||||||||  | || ||||||||||| || ||  ||||||| |||||| |||| |||||||||||  | 
------------------------------------------------------------------------------gtttcct-tgcagttactctttaagatcttcgagtgactg-acgtgcttgtcccagGTATTTATGTGAGCCGCAACACTTACATTCGCGCCGGTGTTGCTGAATGGAAGGTTACGAATCCAGTTCATCTG

upper sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ16610 (Selaginella moellendorffii), 3'ss of exon 4
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                                                                                 || | |   ||||    || |    ||  ||| |||  |  |  |  || ||||| ||||||||||  | || ||||||||||| || ||  ||||||| |||||| |||| |||||||||||  | 
------------------------------------------------------------------------------gtttcct-tgcagttactctttaagatcttcgagtgactgag-gtgcttgtcccagGTATTTATGTGAGCCGCAACACTTACATTCGCGCCGGTGTTGCTGAATGGAAGGTTACGAATCCAGTTCATCTG

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|125272600|gb|EL286685.1|EL286685
EST:     AGTTCGTACTGATG                         GTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGA
genomic: AGTTCGTACTGATGgtaatctttc ... ttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGA
EST: gi|19875109|gb|AU235940.1|AU235940
EST:     TGGATCATGGAGGAAAATGTGGCTTCTTAGATCCAGAGTTCGTACTGATG                         GTCTTTATGTGAGTAGGAATACTTACATTCNAGCTGGAATTGCTGAGTGGA
genomic: TGGATCATGGAGGAAAATGTGGCTTCTTAGATCCAGAGTTCGTACTGATGgtaatctttc ... ttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT
                              aagtaac  putative branch site (score: 2)
                                       tgtatcttcttctc  putative PPT
            ttatatctttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA