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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT

Basic information

species Vitis vinifera
transcript Vv01s0011g00620.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G12930.2 (Glycine max), 3'ss of exon 3
--ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
    |  ||   ||| ||   |         ||| |     |    |   | ||    || |  | | ||| ||  |    |||     |   |  || |||||||||||| || |  |||||||| |||||||||||||||||||| ||||||||||||||  ||||||||||||| || || ||||||            
tcaaattcttctcaacattaatgttgcacagcatctcttgttgg-ttaccacatacttttctttgct-atccttgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAGCAGTCACTAAAAGGATACGAG------------

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 2
ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtt-tatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
  |  || | |   | ||| |  | ||||||        |     ||   |     ||||   |  ||||  |  |    |||     |   |  || |||||||||||| || |  |||||||| |||||||||||||||||||| ||||||||||||||  |||| ||||||||||| || ||||||            
ttatactcttctcaacattaatgt-tgtacaacatctcttgttggttaccacatacttttctttgatatccctgatttcctttattcttcttttgatccagGAAAGGTGATTATTTTCGGTATCTTGCTGAGTTCAAGACTGACCAAGAAAGGAAAGAGGCAGCTGAACAGTCACTGAAAGGATACGAG------------

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 2
---ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtttatctttcctggtgtt--ttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
     |    |||  ||  || ||  | |    |||| |   ||   |  | |    | || |   |||   || | ||   ||  |   |     |  || ||||||||||||||| || || ||||| || ||||||||||| |||||||| || || |||||  ||||||| ||||||||||| || |||            
aaaaaaaatcgtgtcatg-atatatctcttgctattttagcttagcatgcttt----gattctgtatttgatttccttgagcttaatcaattcattttgatccagGAAAGGTGACTATTATCGATATCTAGCCGAGTTCAAGACCGACCAGGACAGAAAGGAGGCAGCTGAGCAATCACTGAAGGGATATGAG------------

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 2
ggaggctgtgcaatatatttacatatgtacatttgaaactaaact--tttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
  ||  |||  | | |    | | || |     |     ||   |  |||   |  |  | | | ||  ||   | |  |   |   |     |  || ||||||||||||||| || || ||| | || ||||||||||| || ||||| || || |||||  ||||||| ||||| ||||| || |||            
aaagattgt-tagtgtcacgatacatctcttgctagttttagcatgctttggttctgtatctgatttcctcgaacttaattaatcaattcatgttgat-cagGAAAGGTGACTATTATCGATATTTAGCCGAGTTCAAGACCGATCAGGATAGAAAGGAGGCTGCTGAGCAATCACTAAAGGGATATGAG------------

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|349830763|gb|FQ417061.1|FQ417061
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|351012160|gb|FQ426882.1|FQ426882
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|110373768|gb|EC938103.1|EC938103
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|351033251|gb|FQ462023.1|FQ462023
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|352789764|gb|FQ478579.1|FQ478579
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|110386347|gb|EC950937.1|EC950937
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
EST: gi|351055188|gb|FQ440527.1|FQ440527
EST:     CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGAT                         GAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG
genomic: CTGATCCCCTCTTCTGGCTCGGGGGAAGCCACTGTGTTCTATTACAAGATgtgagtcatg ... atgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT
           ttttaagtttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaggctgtgcaatatatttacatatgtacatttgaaactaaacttttatatggggttttaagtttatctttcctggtgttttggtatgaatgaattcagGAAAGGTGACTACTACCGGTATCTGGCTGAGTTCAAGACTGACCAGGAAAGGAAAGAGGCCTCTGAGCAGTCACTGAAGGGCTACGAGGCATGTTCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - -ctgtgca
- - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatga