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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgatgtctccttcattctcaggacaattcagaacaaactatcttggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC

Basic information

species Vitis vinifera
transcript Vv14s0108g01170.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G49740.1 (Glycine max), 3'ss of exon 3
gctgatgtctccttcattctcaggacaattcagaacaaact-atcttggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
 | ||   |    || |     | |     |    |    | ||   ||| ||  | | | |  |  |  |  || | | | |      ||  |  ||||||| ||  |||| || |||||||| ||||||||| ||||||||||||| ||||||||||||||||| ||||||||||| ||||||||||| || |||||||
-cagactacctagtcttatgttgaatcccccgattctgtttcattaaggagattctatcgaagttacaagtggataaatttctttgatgattatggtgcagGACACACTGTACTTACATTACGGTAAACAATATTTGAAAGATTGCTACATTGAAGGAAGTGTGGACTTCATCTTTGGCAATAGCACTGCACTTTTGGAGC

upper sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G03050.1 (Glycine max), 3'ss of exon 3
-gctgatgtc-tccttcattctcaggacaattcagaacaaactatcttggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
 | || | |  | |  ||||  | |  |  ||  |   ||      |   |        ||  |||| || || || |   | |  |   ||  |  ||||||| || |||||||| ||||| |||||||||||| |||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| || ||||| |
agatggttttgtacaccattgcctgttctgtttcgtttaaggataatcaaaggaagctatg-gtatcaag-ttgataaacttcttttgtgattatgttgcagGACACGTTGTATTTACATTATGGAAAACAATATTTGAAAGATTGTTACATTGAAGGAAGTGTGGACTTCATTTTTGGTAATAGCACTGCACTCTTGGAAC

upper sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G36950.1 (Glycine max), 3'ss of exon 3
-------gctgatgtctccttcattctcaggacaattcagaacaaactatcttggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
       || | | |  | || | || |||   ||||| |         |   ||||||  | |   |  |  |     || | | | | |    ||  |  ||||||| ||  | || || ||||| || ||||||||| ||||||||||||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||
cagactagccggtctgacgttgaatcccag---aattctgttt----cgttaaggacattctatcaaagttacaagaggataaatttcttccatgattatggtgcagGACACACTATACTTACATTATGGTAAACAATATTTGAAAGATTGCTACATTGAAGGAAGTGTGGACTTCATCTTTGGCAACAGCACTGCTCTTTTGGAGC

upper sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G05650.1 (Glycine max), 3'ss of exon 3
gctgatgtctccttcattctcaggacaatt--cagaacaaactatcttggacatgat--gttgcatatctagc-ttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
         |   | ||| |    || |||  | |  |    |   |||   || ||     | | ||   |  || || |   | |      ||  |  ||||||| ||  | ||||| ||||| |||| ||||||| |||||||||| |||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| |
-----gacttagatgattttgtacaccatttcctgttctgtttcatttgaggataatcaaaggaagataaggtattgataaacttttttcgtgattatgttgcagGACACACTATATTTACATTATGGAATACAATATTTGAAAGATTGTTATATTGAAGGAAGTGTGGACTTCATATTTGGCAATAGTACTGCACTCTTGGAAC

upper sequence: Vv14s0108g01170.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G29090.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------gctgatgtctccttcattctcaggacaattcagaacaaactatc------ttggacatg--atgttgcat--------atctagcttcatg--agtctatccttaaa-tgttta-tgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
                       |  |||  |  |  |  ||   |  || |  |       | |       || ||  ||  || |||||         ||| |   |  |   ||  |||    ||| |||  | |||||||||| |||||||| ||| | || ||||||||| ||||||| || || || || ||||||||||||||||| ||||| || || || ||||| ||||| |
gttcgtttatcagtcctttgattcaaatgatttgtgtaaacttgtggaaactttgtgttggttgttcatagtttagatgtggtatattgcaagtaggttgatccaatcttgttatagcttatttgcaaaatgtgaaatgcagGATACATTGTATTTACATCATGGGAAACAATATTTGAAAGACTGTTACATCGAGGGAAGTGTGGATTTCATATTTGGAAACAGTACCGCTCTCTTGGAAC

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|30252407|gb|CB969958.1|CB969958
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATCTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|30252488|gb|CB970039.1|CB970039
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATCTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|294964344|gb|GW838147.1|GW838147
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|110719767|gb|EE095185.1|EE095185
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAAGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|22013957|gb|BQ798991.1|BQ798991
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|161714142|gb|FC064413.1|FC064413
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|110713332|gb|EE089159.1|EE089159
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|110718638|gb|EE095703.1|EE095703
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|161706131|gb|FC056261.1|FC056261
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAA
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAA
EST: gi|110703355|gb|EE080128.1|EE080128
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAG                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
EST: gi|110718305|gb|EE094986.1|EE094986
EST:     TAACGGCTGATCGTTGTGCCTTCTACAATTGCAAGTTTCTTGGGTGGCAA                         GATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT
genomic: TAACGGCTGATCGTTGTGCCTTCTACAATTGCAGGTTTCTTGGGTGGCAGgtatagtcat ... gtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC
                                       ttaaatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgatgtctccttcattctcaggacaattcagaacaaactatcttggacatgatgttgcatatctagcttcatgagtctatccttaaatgtttatgcagGATACTTTGTATTTGCATTACGGAAAACAATATCTGAAAGATTGCTATATTGAAGGAAGTGTGGATTTCATCTTTGGGAATAGCACTGCTCTGTTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
-ctgatgt
- - - - ctccttc
- - - - - - - - - - -aggacaa
- - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - ggacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgag