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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgaagtcatcttactttgctctaattggagatgattgcttgatgctttcttcccagtgataatatttgttaatgatttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA

Basic information

species Vitis vinifera
transcript Vv09s0002g06040.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G22430.1 (Glycine max), 3'ss of exon 1
tgcttgaagtcatcttactttgctctaattggagatgattgcttgatgcttt--cttcccagtgataatatt---tgttaatgat-ttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA------
            |  || |  |  | || | |    | ||   | || |||     | | | |  |||| ||   |  |||   | || | ||||  || |   || |   ||| |   |||      || | |  || ||||||||||||||| | |||||| ||||||| |||||||| |||||  |  ||||||||||||| |      
------ttactcttctaatcagtgccaacttggttagtttttataattcttcaaactgcaatttgtaatcttctattctaacagtgttcctttaacatggtgacagTTAAATGGGTTGTTTT------ATTGCACAAGATACTCGACTACTGTGTCAAATGATTCTGACACGCATGATGACTTCAAGCCAGCTAATAAGCTTGAGAATTCTG

upper sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G44000.1 (Glycine max), 3'ss of exon 1
-----tgcttgaagtcatc--ttactttgctctaattggagatgattgcttgatgctttcttcccagtgataatatttgttaatgatttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA---
     ||||  || | ||    ||  |   | |  ||    |    |   | ||| |||| |    || | | |||||||       || | ||||  | ||   || |  || | |||  ||  ||   ||||||||| ||||   |||||||  | ||||||||||||||||||||||| |||||  |  ||||||| ||||| |   
attactgctataattgatagactagatgtttttgtttctcaagttgtaggtcatgttttcctttt-gtaacagtatttgtc------ttcctttaatgtcttcacagCTAACTAGGTCCTGTTATCA---TGGAATGAGATACTTTGCTACTGTATCAAATGATCCTGACACACATGATGACTTCAAGCCAGCTAATAAACTTGAGAATT
















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|110362287|gb|EC925809.1|EC925809
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|26265925|gb|CA816988.1|CA816988
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|110382727|gb|EC947047.1|EC947047
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|110382466|gb|EC946757.1|EC946757
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|28959221|gb|CB339611.1|CB339611
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|33409086|gb|CF214713.1|CF214713
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|26263944|gb|CA815007.1|CA815007
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC
EST: gi|110384391|gb|EC948823.1|EC948823
EST:     CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATG                         GTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCAACTACTGTGCCC
genomic: CATTCTTGAAGGGCATCTCCAGCTTCCCATCTGCCCGATTCAGTACAATGgtgagaacta ... ttgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctttcttcccagtgataatatttgttaatgatttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA
                         tgttaat  putative branch site (score: 3)
                 ataatatttgttaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttgaagtcatcttactttgctctaattggagatgattgcttgatgctttcttcccagtgataatatttgttaatgatttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA

tgcttga