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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtatatgtatgtcttgtttcagctatttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT

Basic information

species Arabidopsis thaliana
transcript AT3G19340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
gtaaggtatatgtatgtcttgtttcagctatttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT
     ||| || |   |  | | |||    | |||| | || ||||  ||  |  |   ||| ||           || || |||  |||| ||  | ||| ||||   |||||||||||| || || |||||||||||||||||||| |||||||| ||||| || || |||
-----gtagatctgccttatatctcaaacttctgtt-gaaattttg-aaatctaagaagcaaact-----------atttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 8
gtaaggtatatgtatgtcttgtttcagctatttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT
     ||| || |   |  | | |||    | |||| | || ||||  ||  |  |   ||| ||           || || |||  |||| ||    ||| ||||   |||||||||||| || || |||||||||||||||||||| ||||| || ||||| || || |||
-----gtagatcttccttatatctcaaacttctgtt-gaaattttg-aaatctaagaagcaaact-----------atttttcagGGGAGCCAGAAACAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCCGATATGGAAATAGTTCTT

upper sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 8
------gtaaggtatatgtatgtcttgtt-tcagctatttg--tttgtaactttgtgaacttgtggttca--agcttgt-----ggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT
        |||||   ||| ||   || | || | | || |  |||  |||    || |    |  ||||   || | |     | |   |||  |||||| || ||  |  |   | |||| | ||| |||||||| || || |||||||||||||||||||| |||||||| ||||| || || || 
aaattaccaaggtccttgtctgaagtgctctccgatcttagcatttaaaacaccatggaga-ataattcattggcatctaacaagataggtgactttgcagGCGGGCATGTACGGCAGCAAAACCAGAGCGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTCCTG

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|164120403|gb|ES093533.1|ES093533
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTACTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCT-CTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATT
EST: gi|164162493|gb|ES128661.1|ES128661
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCT-AAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164048125|gb|ES103485.1|ES103485
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAAC-AATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164174603|gb|ES133574.1|ES133574
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGTCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAG-CTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATT
EST: gi|164224291|gb|ES068117.1|ES068117
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCT-AAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|86055111|gb|DR350868.1|DR350868
EST:     AAGCTCACAATACAGGAGCCTACATTCGATAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: AAGCTCACAATACAGGAGCCTACATTCGATAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164223885|gb|ES125727.1|ES125727
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164168438|gb|ES026609.1|ES026609
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164195306|gb|ES166808.1|ES166808
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164179933|gb|ES049443.1|ES049443
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
EST: gi|164237998|gb|ES038674.1|ES038674
EST:     TAGAATGATTGTTGTTTATAG                         ACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT
genomic: TAGAATGATTGTTGTTTATAGgtaaggtata ... gatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT
     ttgtaac  putative branch site (score: 2)
                                        tttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtatatgtatgtcttgtttcagctatttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT