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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG

Basic information

species Vitis vinifera
transcript Vv06s0004g04700.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G04300.1 (Glycine max), 3'ss of exon 4
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG
                                                              | |||      ||      |  || |||  ||  |||  ||||||| | |   |  |  ||  | ||||| || |     | ||||||  ||||||| || ||||| |||||||| |||||||  |||||||| ||||||||||||||||||
--------------------------------------------------------------gtaagactgtgttgcatgatgtgcctca--ttcatttagaaaatgatgtagctccatttgatgtacttttctt-atgcttatagGAACTATAGCTGGCGTTTATGTTGGAATGGAATATGGGGTAGAGAGGATCCGTGGCACCAGAGACTGG

upper sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G41110.2 (Glycine max), 3'ss of exon 4
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG-----------------
                                                              | |||   |  | || ||  | |    |  ||  |||  ||||| | | |   |  |  ||  |  |||| || |     | ||||||  ||||||| || ||||| |||||||| |||||||  |||||||| |||||||||||||| |||                 
--------------------------------------------------------------gtaagactttgtgttgcatgatgtgctacattcatttagaaaattatgtagctccatttgatgtaattttctt-atgcttatagGAACTATAGCTGGCGTTTATGTTGGAATGGAATATGGGGTAGAGAGGATCCGTGGCACCAGAGATTGGGTAATTCTCTCCACAGG

upper sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G41110.1 (Glycine max), 3'ss of exon 4
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG
                                                              | |||   |  | || ||  | |    |  ||  |||  ||||| | | |   |  |  ||  |  |||| || |     | ||||||  ||||||| || ||||| |||||||| |||||||  |||||||| |||||||||||||| |||
--------------------------------------------------------------gtaagactttgtgttgcatgatgtgctacattcatttagaaaattatgtagctccatttgatgtaattttctt-atgcttatagGAACTATAGCTGGCGTTTATGTTGGAATGGAATATGGGGTAGAGAGGATCCGTGGCACCAGAGATTGG

upper sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G33320.2 (Glycine max), 3'ss of exon 4
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG-----------------
                                                              | |||   |  | || ||  | |    |  ||| |||  ||||||  | |   | |    ||     |||  | |     | ||||||  ||||||| || ||| | |||||||| |||||||  |||||||| |||||||||||||| |||                 
--------------------------------------------------------------gtaagactttgtgttacatgatgtgctacatttatttagaaaatgttgtagctcccatttaatgtaattttcttatgcttatagGAACTTTAGCTGGTGTTTATCTTGGAATGGAATATGGGGTAGAGAGGATCCGTGGCACCAGAGATTGGGTAATCCTCTCCATAGG

upper sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G33320.1 (Glycine max), 3'ss of exon 4
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG
                                                              | |||   |  | || ||  | |    |  ||| |||  ||||||  | |   | |    ||     |||  | |     | ||||||  ||||||| || ||| | |||||||| |||||||  |||||||| |||||||||||||| |||
--------------------------------------------------------------gtaagactttgtgttacatgatgtgctacatttatttagaaaatgttgtagctcccatttaatgtaattttcttatgcttatagGAACTTTAGCTGGTGTTTATCTTGGAATGGAATATGGGGTAGAGAGGATCCGTGGCACCAGAGATTGG

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|110362261|gb|EC925781.1|EC925781
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34320123|gb|CF372877.1|CF372877
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|87586971|gb|DY475025.1|DY475025
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110424097|gb|EC990451.1|EC990451
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110713192|gb|EE088900.1|EE088900
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34545250|gb|CF513482.1|CF513482
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110686881|gb|EE063803.1|EE063803
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|83277539|gb|DV941547.1|DV941547
EST:     AAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: AAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|32458600|gb|CD799774.1|CD799774
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110365199|gb|EC927802.1|EC927802
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110380640|gb|EC945923.1|EC945923
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110717262|gb|EE092966.1|EE092966
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34320345|gb|CF373099.1|CF373099
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110384561|gb|EC949005.1|EC949005
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110702521|gb|EE081333.1|EE081333
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110711893|gb|EE088894.1|EE088894
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110381069|gb|EC946383.1|EC946383
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34544205|gb|CF512437.1|CF512437
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGGGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34544118|gb|CF512350.1|CF512350
EST:     CTCGTTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGGGTATGGGGCGGAGAGGATTC
genomic: CTCGTTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34545330|gb|CF513562.1|CF513562
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110385580|gb|EC950119.1|EC950119
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|110378520|gb|EC943657.1|EC943657
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
EST: gi|34545089|gb|CF513321.1|CF513321
EST:     TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG                         GAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC
genomic: TTGAAGAAGATGTGCAAAGAAGCTGCATATTGGGgtaagcataa ... acatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG
                                 ctccttttgttcac  CT-rich tract
          aaaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcataagcagttttgcatactgtaacttattgaaaaaaacctgttttgtacgaggcatgaaagctatctttttccagtaagcttcagttttctttgcaaaatgaggaacaacactgagaactccttttgttcacatcaacagGAACCGTAGCTGGAGTATATGTGGGAATGGAGTATGGGGCGGAGAGGATTCGTGGCACCAGAGACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT