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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttacaattttctgtgcctatcaataaaagtgaacaaaaaacatgtaacaattttcttcatttgtttattaagatctaatatttgtctgtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATTTTTACCTGGATTGGCACAATCATGGGTGGAAATGGAACTGTGTATGAGG

Basic information

species Vitis vinifera
transcript Vv13s0019g04090.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G31920.1 (Glycine max), 3'ss of exon 2
----tctttacaattttctgtgcctatcaataaaagtgaacaaaaaacatgtaacaattttcttcatttgtttattaagatctaatatttgtctgtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATTTTTACCTGGATTGGCACAATCATGGGTGGAAATGGAACTGTGTATGAGG
       |||||| |   |   ||  | | | | | |  | |      || |     |     ||| |       |||   || ||| |    | ||    ||||||||||||||||||||||||||||| ||||| |||||  | ||||| |||||||| ||||||||||||||    |||||||| || ||| |||||||||
taaggtgttacaaatgcttt--ccctttagtcatattata-atttgttatcttgttctcacagtcactaacactctaaatgctgataataactt-ttcctgcagATGAGTGGAGGAGATCTTGGGGTATCGGCTTTTCCTGATGGGGAGAGTATTTTTACATGGATTGGCACAATTGAAGGTGGAAAAGGGACTCTGTATGAGG

upper sequence: Vv13s0019g04090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G35630.1 (Glycine max), 3'ss of exon 2
tctttacaattttctgtgcctatcaataaaagtgaacaaaaaacatgtaacaattttct-----tcatttgtttattaagatctaatatttgtctgtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATTTTTACCTGGATTGGCACAATCATGGGTGGAAATGGAACTGTGTATGAGG
    ||   |||          |   |   ||| |    | ||  ||| |   | ||||     ||| |     | | |    | ||| |    | ||    |||||||||||||||||||| ||||| || ||||| |||||  | ||||| |||||||| ||||||||||||||    |||||||| || |||  ||||||||
----taaggtttcacaaatgctttgcttttagtcatattataatttgttatcttgttctcacagtcactaacacactcaatgttgataatgagtt-ttcctgcagATGAGTGGAGGAGATCTCGGGGTGTCGGCTTTTCCTGATGGAGAGAGTATTTTTACATGGATTGGCACAATTGAAGGTGGAAAAGGGACTCAGTATGAGG
















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|161721358|gb|FC070758.1|FC070758
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|161718960|gb|FC066380.1|FC066380
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|294965000|gb|GW838803.1|GW838803
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|161712977|gb|FC062103.1|FC062103
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|37186163|gb|CF605516.1|CF605516
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|110426829|gb|EC993253.1|EC993253
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|161720059|gb|FC065103.1|FC065103
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|110711177|gb|EE087407.1|EE087407
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|30125638|gb|CB910977.1|CB910977
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
EST: gi|110686046|gb|EE063296.1|EE063296
EST:     GCTTCAAAAAGAGTTGATGGCCCTCATG                         ATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT
genomic: GCTTCAAAAAGAGTTGATGGCCCTCATGgtatattcat ... gtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaacaattttcttcatttgtttattaagatctaatatttgtctgtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATTTTTACCTGGATTGGCACAATCATGGGTGGAAATGGAACTGTGTATGAGG
                              atctaat  putative branch site (score: 3)
                                          tctgttt  putative PPT
      aattttcttcatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttacaattttctgtgcctatcaataaaagtgaacaaaaaacatgtaacaattttcttcatttgtttattaagatctaatatttgtctgtttgcacagATGAGTGGAGGAGATCTTGGGGTATCTGCTTTCCCTGAAAGCGAGAGCATTTTTACCTGGATTGGCACAATCATGGGTGGAAATGGAACTGTGTATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - tgcctat
- - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - gtaacaa