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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtttttctatgatttctcatttctatgcaaaccccatttcttcttttagcttgtaaactcagaaactggttccattatcattaatattattttcttttgcatgttgttttgttttttggatgtagtattgtaggatatttctagggttactcatatgatcgatttgtgttaaaatgggggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAATGGCTCAGAAGAACAGCAGCGAGGAGGGTGAGAAGGGAAGCAGCGGTGCT

Basic information

species Vitis vinifera
transcript Vv05s0020g04690.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G32340.1 (Glycine max), 3'ss of exon 1
gtatgttgtttttctatgatttctcatttctatgcaaaccccatttcttcttttagcttgtaaactcagaaactggttccattatcattaatattattttct-tttgcatgttgttttgttttttggatgtagtattgtaggatatttctagggttactcatatgatcgatttgtgttaaaatgggggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAATGGCT---CAGAAGAACAGCAGCGAGGAGGG---TGAGAAGGGAAGCAGCGGTGCT
                                                                             || ||||||| |  ||| || | |  |||||||   ||   ||||     ||  | ||||  |   |      | | ||    ||  |   ||||||   ||||||       ||||||||| || ||||| ||||||||||||||  ||||||  ||||||||||| |||||    ||||||   ||||  ||||| |    |||||||  ||  |||      
--------------------------------------------------------------------------ttatctattatcaatgttataatatacagtttgcataaggt---gtttgcaacataca-tattagaaagtg-----aagattg---atggg---gatttggaataaaat-------tttcagGGCTCAAGTGGTTGGTTGGCCACCAGTGAGATCATACAGGAAGAACATGATGGCAGTACAGAAGGTTAGCAATGAGGAAGTAGCTGAGAAGACAACAAGC------
















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|110701227|gb|EE078570.1|EE078570
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351045653|gb|FQ440838.1|FQ440838
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|34548112|gb|CF516344.1|CF516344
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351031102|gb|FQ444929.1|FQ444929
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351026381|gb|FQ428393.1|FQ428393
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|110362275|gb|EC925796.1|EC925796
EST:     GAGAAGAACCTCCTTCGTTGCACCAAGGATCCGGCCAAACCACCTGACAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351022932|gb|FQ428841.1|FQ428841
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGCTCGATCATTTAGGAAGAACGTAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|34550158|gb|CF518376.1|CF518376
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|161711187|gb|FC058260.1|FC058260
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|110390251|gb|EC955151.1|EC955151
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|110390209|gb|EC955109.1|EC955109
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|161717057|gb|FC069543.1|FC069543
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|34548138|gb|CF516370.1|CF516370
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351045641|gb|FQ440826.1|FQ440826
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|349808827|gb|FQ406677.1|FQ406677
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|110382108|gb|EC938506.1|EC938506
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|161718466|gb|FC067305.1|FC067305
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|34549663|gb|CF517895.1|CF517895
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|27578902|gb|CB001597.1|CB001597
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|110378509|gb|EC943646.1|EC943646
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|34551059|gb|CF519257.1|CF519257
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|351056255|gb|FQ453717.1|FQ453717
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|161717681|gb|FC066282.1|FC066282
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|161712844|gb|FC062019.1|FC062019
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
EST: gi|30328414|gb|CD011676.1|CD011676
EST:     GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAA                         GGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT
genomic: GAGAAGAACCTCCTTCCTTGCACCAAGGATCCGGCCAAACCACCTGCCAAgtatgttgtt ... ggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatttctagggttactcatatgatcgatttgtgttaaaatgggggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAATGGCTCAGAAGAACAGCAGCGAGGAGGGTGAGAAGGGAAGCAGCGGTGCT
                                                ctttc  CT-rich tract
                            atttgtgttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgtttttctatgatttctcatttctatgcaaaccccatttcttcttttagcttgtaaactcagaaactggttccattatcattaatattattttcttttgcatgttgttttgttttttggatgtagtattgtaggatatttctagggttactcatatgatcgatttgtgttaaaatgggggactttcagGGCACAGGTGGTGGGTTGGCCACCAGTTCGATCATTTAGGAAGAACATAATGGCTCAGAAGAACAGCAGCGAGGAGGGTGAGAAGGGAAGCAGCGGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG