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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G13670.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
-----gttgtctgatgtttctctgttagt--------tatttttatatctgtgttctgtcaagatga-tcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
      || | |||| | | |   | |||        |||  |||  | | |||| |   | ||||| |||| |||| ||     ||||||||    |||||||||||| ||||| ||||||||||||||||| ||||||| ||||||||| || || |  ||||| |||||  | || || ||||||||||
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcatatgatgaatcttgcctgtga-----ttctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 12
----gttgtctgatgtttctctgttagttatttttatat--------ctgtgttctgtcaagatga-tcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG-
     || | |||| | | |   | |||  || | ||||         | |||| |   | ||||| |||| ||   | |   |||||||||    |||||||||||| ||||| |||||||| |||||||| ||||||| ||||||||| || || |  ||||| |||||  | || || |||||||||| 
tgaaattatatgatttatataaatcagtacttgtcatataattagctatctgttttcatatgatgaatcttgcccatgtg---attctgtttcttttcaggAATGGATCATGGAACAGTGGGAAAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTTGTGGTGATGTCAAAAGG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 12
--gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
  |   | || ||| | |||   |||| | |||| ||||   |||  |     | | |||| |   |  ||| |  || ||||   ||||||||||| |||||||||||||| || ||||  ||||||| ||||||||| ||    | |||||| |||||  | || || ||||||||||
gtgaaatatgctgtatgtcttgcagtt-tcttta-atcta-attccatgtgattaaacttatccatg--tgactgttgctttg---cagGAATGGATAATGGAGCAGTGGGATAAAAACTTTTACATTACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 12
--gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
  |   | || ||| | |||   |||| | |||| ||||   |||  |     | |  ||| |   |  ||| |  || ||||   |||||||||||||||||||||||||| || ||||  ||||| | ||||||||| ||    | |||||| |||||  | || || ||||||||||
gtgaaatatgctgtatgtcttgcagtt-tcttta-atcta-attccatgtgattaaaattatccatg--tgactgttgctttg---cagGAATGGATTATGGAGCAGTGGGATAAAAACTTTTACATCACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 12
----------gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaa-gatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
          | ||||    |||| |   ||  | |||  |  || |   |  |   ||  || ||  ||  | ||  | | || | |     | ||||||||||||||||| || ||||||| |||||  || || ||||| ||||||||||| | ||||||||| ||| | ||||| ||||| ||||
gtgatattctggtgtccatagttttttattttttaattagttaattttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
                                   | | ||  | || || |||   |  |   | | || |   |||| | |  |   |  ||| | | ||| |  | |||| |  ||||| ||||| ||||| |||||||| ||||| | ||| || ||| | || ||||||||||  || ||||||||||| || |||||||| ||||
gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtc-gttcaatgatagaacagctat-ccctgttatg-cgccatgccctcacattgagtcatattttta--cagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 9
gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG---------
                        || ||||          | | || ||    ||| || |     ||    ||||    ||  |||||||||| ||||||||||||||||||||||||||||| ||  | || || ||||| | ||| || |||||  | || || ||||| || |         
--------------------gtactacttttgacgaaacaatttttcgaggct-tctcacatttctctgctgcctgtc---aa--agGAATGGATCATGGAGCAGTGGGAGAAGAACTACTACATCAGCGCAATCGCCGGTGCCAACAACGGTAGCTCGCTGGTGGTGATGTCCAAGGGAACGTCCT

upper sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
                          ||   | |||| || |         | |||||     | ||   |||||  |  |   ||||| ||||| ||||| || |||||||| |||| |||||||||| | ||||| || || | ||| || |||||  | ||||||||||||||||
-------------------------gttagcacatct-tgcttaactttagtaatcttc----atagctcattctcctcgg---cagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

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|86059947|gb|DR355704.1|DR355704
EST:     CTGGCTTCACGCACCAAGTCTATGAACTCTCTCCTGTATTCTTGCACAAG                         GAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCT
genomic: CTGGCTTCACGCACCAAGTCTATGAACTCTCTCCTGTATTCTTGCACAAGgttgtctgat ... tttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG
                     atcttac  putative branch site (score: 3)
                                       ttctgtttt  putative PPT
                                            ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtctgatgtttctctgttagttatttttatatctgtgttctgtcaagatgatcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG