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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtttggttctggcttagcattactgtattatggtttgaatggctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA

Basic information

species Vitis vinifera
transcript Vv17s0000g01720.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 1
----ttggtttggttctggctta-gcatta-ctgtattatggtttgaatggctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
    ||  |        || ||| | ||||  |||||      || | | |  || || ||  ||||| |    |||  ||  ||||| |||   || || | ||||  |  | ||||||||| |||||| | ||||||||   ||  | |||||||| ||||||||||||||| ||||||||||||||||     | || |||||
tttttttatggaaacagggtttaagtattagttgtatgtcttgttaacttgaattctttttaattttttg----tatgttgctcatttttttt--tgaatgttcagGCATATTAACTGATGAGCTGAGGACTGTCTTGGAGACCAACTTGCCTAAAGTGAAGGAAGGTAAGAAGTCCAAGTTCAGTTTAGGTGTGTCCGATCCTAA

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 1
--------ttggtttggttctggcttagcattactgtattatggtttgaatggctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
        ||  |||  |||      |  | | | |||   ||    |||||    || |  |  |  || ||   |||     | |||||      ||      |||||||  ||||||||||| |||| |   | ||||||  |||  | |||||||| ||||||||||||||| ||||||||||||||||     | || || ||
tttttttttttttttttttcacaaaaaaaaatgccgtaaagtgtcccgaatgataatgatgatgatgatttgg---tattgattatatttg-----gtgttcaatcagGGCTGTTGACTGATGAGCTGAGAACGGTTTTGGAGACTAACTTACCTAAAGTTAAGGAAGGTAAGAAGTCCAAGTTCAGTTTAGGTGTATCGGATCCAAA

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 1
ttggtttggttctg-gcttagcattactgtattatggtttgaatggct-ttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
||   ||  || |  |   |   |||    |  | |  || | |     ||||   || | | |  |  ||  | |     ||| |||   |  || | ||||  |  | ||||||||| |||||| | | ||||||  |||  | |||||||| ||||||||||||||| ||||||||||||||||     | || |||||
ttaccttttttatatggagaagcttatccaaacaggaattaagtcatagttgtgtgtcttgtatatgttgttcattt--tctttttttatttttatgttcagGCATATTAACTGATGAGCTGAGGACTGTTTTGGAGACTAACTTGCCTAAAGTGAAGGAAGGTAAGAAGTCCAAGTTCAGTTTAGGTGTGTCCGATCCTAA

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 1
ttggtttggttctggcttagcattactgtattatggtttgaatggctttgttattcctttttggggagtataatggacatttgtttgaatgg---atttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
 |  |||     ||  |     ||  ||| || || |||   |  | ||||| |   ||| |      |    | |  ||| |||| ||||    |||   |||  |||||||||||||| | || |||||  ||||| | ||||||||||| |||||||| || ||||| ||||||||||||||||||   || || |||||
-taatttatggttgattct-tgtttttgtgttctgtttttgttt-cattgttttggttttgtcattgatgcttttggaattggttttaatgtgatattggtagGTGTTATGACTGATGAGCTTAGAAGTTTTCTGGAGTTGAATCTTCCTAAGGTCAAGGAGGGAAAGAAACCCAAGTTCAGTTTAGGATTGGCTGAGCCTAA

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 1
ttggtttggttctggcttagcattactgtattatggtt---tgaatggctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
   ||| |  || |  |   |  | |||| |||   ||   || | | |||  | ||    | ||      | || ||    |     | ||   | |   |||    ||||  |||||| |||| |||||  ||||||| ||||| || ||||| |||||||| |||||||||||||| ||||| |||    | || |||||
-ctgttggaatcagcttattctgttctgttttagcttttgctggaggtcttgataataaagtattaatatttgtattgtttttacaccttaa--aaatcgtagGATACATGAGCGATGAGCTGAGAAGTTTTCTGGAGCTGAATCTCCCGAAAGTGAAGGAAGGCAAGAAGCCCAAGTTTAGTTTGGGAGTGTCTGAGCCTAA

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|71864289|gb|DT013344.1|DT013344
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|110712950|gb|EE088442.1|EE088442
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCGATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|110686032|gb|EE063274.1|EE063274
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|71861748|gb|DT010803.1|DT010803
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|110690304|gb|EE067284.1|EE067284
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|110718517|gb|EE095438.1|EE095438
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|71865133|gb|DT014188.1|DT014188
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|161719328|gb|FC068961.1|FC068961
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|110701410|gb|EE078950.1|EE078950
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|161720525|gb|FC070912.1|FC070912
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|71857394|gb|DT006449.1|DT006449
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
EST: gi|294965620|gb|GW837219.1|GW837219
EST:     GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAG                         GGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG
genomic: GTTTGAATCCGCTCTCGATGCTCTGAATCAATGCAACTCAGTGTCTGAAGgtgagaattt ... ggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA
                                                tttcc  CT-rich tract
                     agtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtttggttctggcttagcattactgtattatggtttgaatggctttgttattcctttttggggagtataatggacatttgtttgaatggatttccagGGCTTATGACTGATGAGTTGAGGAGTTTCTTGGAGCTTAATCTTCCTAAAGTCAAGGAAGGTAAGAAGCCCAAGTTCAGTTTAGGAACTGCAGAACCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- ggtttgg
- - - - -ttctggc
- - - - - - - - - - - - - - - - - - - tgaatgg