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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAATTGCCCGAGCCTATGAGAAAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataatttggcagttctctttctaacttaatatcaccagatttcattaccttattggtggtaagcagttggatattggatatagaagtaagcttttttccctaaccacctttattttcttttgctttatgttattcaag

Basic information

species Vitis vinifera
transcript Vv12s0057g01240.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G42680.1 (Glycine max), 5'ss of exon 4
GTTGAAATTGCCCGAGCCTATGAGAAAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataatttggcagttctctttctaacttaatatcaccagatttcattacct-tattggtggtaagcagttggatattggatatagaagtaagcttttttccctaaccacctttattttcttttgctttatgttattcaag
|||||||||||   ||| |||||||||||||||||||| ||||| ||||||||||| ||||| |||||||||||||||                           || |   |  || ||  |||| | || || | |  |  | |||| |    |||  || | ||||   | || |  ||| |  || | | | | ||     || ||  || ||
GTTGAAATTGCTAAAGCTTATGAGAAAGGTGGAGCAGCATGTCTAAGTGTTTTGACAGATGAAAAGTATTTTAAGgtaga-----------------------ccaacacacctggaatttgttacgtgtactgctagataatatttggct----gattcagtactaagtgatattgc--aacaaaattaactctatctta----atattggtccag

upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G05810.2 (Glycine max), 5'ss of exon 4
GTTGAAATTGCCCGAGCCTATGAGAAAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaa-taatttggcagttctctttctaacttaatatcaccagatttcattaccttattggtggtaagcagttggatattggatatagaagtaagcttttttccctaaccacctttattttcttttgctttatgttattcaag
|||||||||||    || |||||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||   |     |       ||  ||  |   ||   | ||||   | ||  |   || |      |     ||||||| | | | || |||   |   |   ||     |                              
GTTGAAATTGCTAAGGCTTATGAGAAAGGTGGAGCAGCATGTCTAAGTGTTTTGACAGATGAAAAGTATTTTAAGgtaaaccaacaaacctggaatttgttatgtgtgtactgctagat---aatatttggctgattcagtactaggtgatattgca-acaaaattaactctaacttaatattggtccag---------------------------
















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|351046192|gb|FQ442570.1|FQ442570
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351031552|gb|FQ459809.1|FQ459809
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAA
EST: gi|351031792|gb|FQ460049.1|FQ460049
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATA
EST: gi|351033918|gb|FQ462973.1|FQ462973
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATG
EST: gi|110421432|gb|EC987728.1|EC987728
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|349821059|gb|FQ404312.1|FQ404312
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGA-GTATTTTAAG                         GGAAACTTTGA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGA
EST: gi|110687718|gb|EE065446.1|EE065446
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGTAAATCTGGAGTTGATACGAAATGCCGGAAGTAA-G
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGA-GTAAAG
EST: gi|352795534|gb|FQ480122.1|FQ480122
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|352789729|gb|FQ478544.1|FQ478544
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAAGT-GATACGAAA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGA-GTTGATACGAAA
EST: gi|110697753|gb|EE075019.1|EE075019
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351053257|gb|FQ459125.1|FQ459125
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351045623|gb|FQ440808.1|FQ440808
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAAT
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAAT
EST: gi|110691072|gb|EE068758.1|EE068758
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|352798538|gb|FQ480563.1|FQ480563
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGG-AGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351046111|gb|FQ442489.1|FQ442489
EST:     AAGGTGGAGCAGCTTGTCTTAATGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACAAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351054706|gb|FQ462736.1|FQ462736
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAATATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGA
EST: gi|110724707|gb|EE100769.1|EE100769
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAAGCTT-GAAAATCTGGGAGT-GATACGAAATGCCCGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAA-GCTTTGAAAATCTGG-AGTTGATACGAAATGCCGGAGTAAAG
EST: gi|110709662|gb|EE085318.1|EE085318
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351044450|gb|FQ442981.1|FQ442981
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATAC
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATAC
EST: gi|161713572|gb|FC063401.1|FC063401
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351057250|gb|FQ450957.1|FQ450957
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGAAGCTTTGAAAAT
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAAT
EST: gi|351036912|gb|FQ459434.1|FQ459434
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTCTAAG                         GGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGATACGAAATGCCGGAGTAAAG
EST: gi|351031889|gb|FQ460146.1|FQ460146
EST:     AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAG                         GGATGCTTTGAAAATCTGGAGTTGA
genomic: AAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataattt ... gttattcaagGGAAGCTTTGAAAATCTGGAGTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAATTGCCCGAGCCTATGAGAAAGGTGGAGCAGCTTGTCTTAGTGTTTTGACTGATGAGAAGTATTTTAAGgtaataatttggcagttctctttctaacttaatatcaccagatttcattaccttattggtggtaagcagttggatattggatatagaagtaagcttttttccctaaccacctttattttcttttgctttatgttattcaag

- - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT