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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctgattccacccttcaagtttagcaatctgtaaatatttaaatcacgccgattgttgctgtgttttgtctgaattctgtgtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGACGATAATGGGTCCAATCCCAGCTGTCAAATATGATGAGTCAAGACAAAGG

Basic information

species Vitis vinifera
transcript Vv09s0002g03450.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03450.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G02280.1 (Glycine max), 3'ss of exon 2
---gtttctgattccacccttcaagtttagcaatctgta---aatatttaaatcacgccgattgt-tgctgtgttttgt-ctgaattctgtgtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGACGATAATGGGTCCAATCCCAGCTGTCAAATATGATGAGTCAAGACAAAGG
    ||||| | |  |  ||  |  |  |   | || ||    || | |  |  |     ||    |    | ||  ||  || | | | ||  | |||||||| ||| | ||||| ||||||||||| ||| |||| ||||| ||||||||  | ||||||||||| || |  || ||||||||||||   |||||| | 
taattttctaacttgaaactaaacatgcacacacctttatttgatttatggaaaagaagaataaaataaaatattgggtattggaatgtttgcat-tgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGACAGTCATGGGTCCAATTCCGGGCGTTAAATATGATGAGAGGAGACAACGA
















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|351056398|gb|FQ454259.1|FQ454259
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|34547124|gb|CF515356.1|CF515356
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|34551064|gb|CF519262.1|CF519262
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCCGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|351047992|gb|FQ441164.1|FQ441164
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|30329448|gb|CD012710.1|CD012710
EST:     AAACCACAGCTGAGAAGAG                         GGCTGCTCAGGTGGGAATGAAGTTGGAGTGGATGGAAGATGGAGTGAAGAC
genomic: AAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|351031694|gb|FQ459951.1|FQ459951
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGGGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110375915|gb|EC940945.1|EC940945
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|34547213|gb|CF515445.1|CF515445
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|352789732|gb|FQ478547.1|FQ478547
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110686256|gb|EE063694.1|EE063694
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|349814631|gb|FQ399271.1|FQ399271
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAAAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGCTGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110363879|gb|EC927508.1|EC927508
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110390279|gb|EC955181.1|EC955181
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|349833013|gb|FQ416391.1|FQ416391
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|351019404|gb|FQ429539.1|FQ429539
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|349808849|gb|FQ406699.1|FQ406699
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAAGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|351043769|gb|FQ431321.1|FQ431321
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110401242|gb|EC967845.1|EC967845
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110396768|gb|EC962467.1|EC962467
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110421556|gb|EC987854.1|EC987854
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|349829847|gb|FQ422160.1|FQ422160
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|46918186|gb|CN547515.1|CN547515
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110385809|gb|EC950365.1|EC950365
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110413219|gb|EC978998.1|EC978998
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAAGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110713963|gb|EE090343.1|EE090343
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACGGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAATTGGAGTGGATGGAGGATGGAATGAAAAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC
EST: gi|110401052|gb|EC967645.1|EC967645
EST:     GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAG                         GGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGAGTGAAGAC
genomic: GGCTGGAAGTCCACATTCCTGACCCAGGATAAAACCACAGCTGAGAAGAGgtttctgatt ... gtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaaatcacgccgattgttgctgtgttttgtctgaattctgtgtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGACGATAATGGGTCCAATCCCAGCTGTCAAATATGATGAGTCAAGACAAAGG
                                            tgtctct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctgattccacccttcaagtttagcaatctgtaaatatttaaatcacgccgattgttgctgtgttttgtctgaattctgtgtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGACGATAATGGGTCCAATCCCAGCTGTCAAATATGATGAGTCAAGACAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG