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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttacttattcactttttcctccatttgatgcatagatagctctacggaatgacatcattcaaaactagtgtagt...

Basic information

species Vitis vinifera
transcript Vv04s0044g01840.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA09G32820.1 (Glycine max), 5'ss of exon 10
AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttact-tattcactttttcctccatttgatgcatagatagctctacggaatgacatcattcaaaactagtgtagt---------
||||||||||| ||||| ||||||||||||||||| |||||||| || ||||||     ||   ||    | ||||||  || || | | | | | ||    ||||  | |       |  | || |  |   ||  || | ||| | | ||         
AAAGATTGTTTTGAGGTCTATGCTTTAGTTCCTGGCCTTCTGCGGGAAGAGgtaataagct---gagttatgctttttctctgtaataattctgtacttttgttgaaactt------tttcatggtaaaatggcaagcata-ctaatattgtcatcctcct

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA16G21840.2 (Glycine max), 5'ss of exon 12
AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttacttattcactttttcctccatttgatgcatagatagctctacggaatgacatcattcaaaactagtgtagt---------
||||||||||| ||||| ||||||||||||||||| |||||||| || ||||||     ||     |    | ||||||   | | || |  |||     |||  ||  || |    |  | |  |  | | ||  || | ||| | | ||         
AAAGATTGTTTTGAGGTCTATGCTTTAGTTCCTGGCCTTCTGCGCGAAGAGgtaataagct----gagttatgtttttt--ctgtgcaataattctgtacttt--tgtttaaactttttcatgataaaatagcaagcata-ctaatattgtcatcgtcct

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G09370.1 (Glycine max), 5'ss of exon 11
AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttacttattcactttttcctccatt-tgatgcatagatagc-tctacggaatgacatcattcaaaactagtgtagt
||||||||||| ||||| ||||||||||||||||| || ||||| || ||||||||  | ||  |      | | |||   ||||     ||   ||   || ||||| | |   ||| | |      ||  ||   ||        |  || 
AAAGATTGTTTTGAGGTATATGCTTTAGTTCCTGGCCTACTGCGGGAAGAGgtatg-cattctggttgttatatatttcttttatctgtattaatctgtgttgtgatgaaaattaagcatatcatttttgctatttctctccttcctttgag-

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G09370.2 (Glycine max), 5'ss of exon 10
-------------------------------------------------AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttacttattcactttttcctccatt-tgatgcatagatagctctacggaat-gacatcattcaaaactagtgtagt
                                                 ||||||||||| ||||| ||||||||||||||||| || ||||| || ||||||||  | ||  |      | | |||   ||||     ||   ||   || ||||| | |   |||    |    | |  ||   ||        |  || 
ATGAGTCATATATGTAATTCCTTATTTCAATGAAAACTCTTCTGTGCAGAAAGATTGTTTTGAGGTATATGCTTTAGTTCCTGGCCTACTGCGGGAAGAGgtatg-cattctggttgttatatatttcttttatctgtattaatctgtgttgtgatgaaaattaagcatatcatttttgctatttctctccttcctttgag-

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA01G36040.1 (Glycine max), 5'ss of exon 11
AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatg-gtactcctgaaaccttcttttttacttattcactttttcctccatttgatgcatagatagc-tctacggaatgacatcattcaaaactagtgtagt
||||||||||| ||||| ||||||||||||||||| || ||| | || ||||||||  | ||  |         | |||||  | |     | |   |   | ||||| | |  |||| | |      || |||   ||        |  || 
AAAGATTGTTTTGAGGTATATGCTTTAGTTCCTGGCCTGCTGAGGGAAGAGgtatgcattctggttgttatacttcttttatctgtattaatctgtgttgttgtgatgaaaatttagcatattatttttgccatttctccccttcctttgag-

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|30131007|gb|CB916346.1|CB916346
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|56409766|gb|CX018018.1|CX018018
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|110703600|gb|EE080590.1|EE080590
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|351041413|gb|FQ447540.1|FQ447540
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|110374828|gb|EC939763.1|EC939763
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|110691152|gb|EE068926.1|EE068926
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|110711713|gb|EE088506.1|EE088506
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|34363693|gb|CF405278.1|CF405278
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|56409464|gb|CX017716.1|CX017716
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|56409535|gb|CX017787.1|CX017787
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|46911394|gb|CN546769.1|CN546769
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|352794399|gb|FQ481630.1|FQ481630
EST:     AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|30302776|gb|CB979570.1|CB979570
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACCA
EST: gi|71880737|gb|DT029792.1|DT029792
EST:     AAGATTGTTTTGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAG                         GTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACC
genomic: AAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtact ... gcaaactcagGTGAGGGTTCAATCAGATCCAGCAGGGCGGTTAGTTATAACCGGGGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGATTGTTTCGAGGTTTATGCTTTAGTTCCTGGGCTTCTGCGAGAGGAGgtatggtactcctgaaaccttcttttttacttattcactttttcctccatttgatgcatagatagctctacggaatgacatcattcaaaactagtgtagt

- - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaactag