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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG

Basic information

species Vitis vinifera
transcript Vv19s0014g02310.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctt--tctggtttctgaattt-tatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
                  |   |   ||    || |  | |   |      |  |  | || || |  |   |||  |    ||| | |  |  | ||   | || | ||  ||   | ||   |   | ||||||||||||||||| |||||||| |||||||||||||| || |||||||| |||
----------------gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 7
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
          ||| |   ||| ||         | ||| || |  ||      ||  |||   |    || |  |  |||| ||   |  |||  | |  | || ||  ||   | ||   |   | ||||||||||||||||| |||||||| ||||| |||||||| || |||||||| |||
--------gtatgtt---atattctgacaggttatatccaatttgttt-----attttatgatttcattgaaaaatgatgcatgtaataatttgagata-cggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTGACAAGGACTATATCAAGGAGAAAG

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G36130.2 (Glycine max), 3'ss of exon 6
---------gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgct--cttctttctggtttctgaattttatgt----ttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
          || ||   || |||  |||     |||       | |  ||   ||  || ||||  |||||||| ||   |    ||| |  ||  | |   | ||  |    | || |||||    || |||| || | |||||||||||||||||| |||||||| || |||||||| || || |||||||| |||
gtatgtgtcttattctgagaggctataatccaattttttttatgaccagacgacttcaaaaaatg--atacataaaataatttgagatgtgaactaacatgcatttgcatatgaatttctatgtgattttgtgactttcttacagGTTGCAGATTTTGGTGTTTCTGCACAGTTAACAAGAACTATATCAAGGAGAAAG

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 7
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctataca-taatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
            | |    || |  | |    | |    |  |||    || | | | | | | |   ||   ||| |   | |||  ||   | ||  ||     | | || ||| |||| || | |||||||||||||||||| |||||||| || |||||||| || || |||||||| |||
------------gtttgtgtatttttataagactagaggacttcaa-aaaacagtacaaaataatttgatacgtgaactaacatgcatttgcatatgaatttc---tgtcat-tttgtgactttcttacagGTTGCAGATTTTGGTGTTTCTGCACAGTTAACAAGAACTATATCAAGGAGAAAG

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 6
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
                                                                         |    |||||| | |      | ||   || | |  || |||       |  ||||||||||||||||||| |||||||| ||  | ||| | ||  | || | | |||| 
-------------------------------------------------------------------------gtaactgcgtggtttagaaggtcgtgattgtactc-atattt-----tataaaacagGTTGCAGATTTTGGGGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAA

upper sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 6
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgacct-tgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
                                                                              |   |||     ||    | || |||   || |  |  |    | |  ||||||||||||||||||| |||||||| ||  | ||| | ||  | || | | |||| 
-----------------------------------------------------------------------------gtaactgcgtggtttagaaggttgtga---ttgtactcatattttataaaacagGTTGCAGATTTTGGTGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAA

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|352772708|gb|FQ473746.1|FQ473746
EST:     CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG                         GTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAG
genomic: CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGgtaatccttg ... cttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAG
EST: gi|71861562|gb|DT010617.1|DT010617
EST:     CGGCAAACATTTTGTTGACTGAGAATGGTGATGTTAAG                         GTTGCAGATTTTGGCGTTTCTGCACAATTAACAAGGACAATCTCAAGGAGG
genomic: CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGgtaatccttg ... cttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGG
EST: gi|352768969|gb|FQ468160.1|FQ468160
EST:     CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG                         GTTGCAGATTTTGGCGTTTCTGCGC
genomic: CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGgtaatccttg ... cttgtaacagGTTGCAGATTTTGGCGTTTCTGCGC
EST: gi|352781734|gb|FQ469032.1|FQ469032
EST:     CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG                         GTTGCAGATTTTGGCGTTTCTGCGCCATTAACCAAG-ACAATCTCAAGGAG
genomic: CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGgtaatccttg ... cttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAAC-AAGGACAATCTCAAGGAG
EST: gi|352781360|gb|FQ468204.1|FQ468204
EST:     CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAG                         GTTGCAGATTTTGGCGTTTCTGCGCAA
genomic: CGGCAAACATTTTGTTGACTGAGAATGGCGATGTTAAGgtaatccttg ... cttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
                                      ttctgac  putative branch site (score: 2)
                      tttctgaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctttctggtttctgaattttatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA