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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCTTCTGGACCATTTAGCAATGATTACAGTTCATTCAGATTCTCGTGGGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatattccatttttttttttcctcccctagtttttcttttctcttcgtcttcatcaaatccatagctggttaaataagtctttattaaagaaaagg...

Basic information

species Vitis vinifera
transcript Vv12s0035g00640.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G30160.1 (Glycine max), 5'ss of exon 5
AGCTCTTCTGGACCATTTAGCAATGATTACAGTTCATTCAGATTCTCGTGGGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatattccatttttttttttcctcccctagtttttcttttctcttcgtcttcatcaaatccatagctggttaaataagtctttattaaagaaaagg
 || ||||| |||||  | |||||||| || |||||  |   ||||||||||  ||||||||||||||| ||||||||||| |||| | | || |||||||| | ||  |  || || |    |   |    |     | | || ||||  |    |   ||        || |   |||  | || | | |   |  | 
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGGGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtataattatgaatattatgcaataaactaacatgccatttattttcttaatggaaagttaacaggagtatgttagcatatttgttcaatcatacattgc

upper sequence: Vv12s0035g00640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G13320.1 (Glycine max), 5'ss of exon 5
AGCTCTTCTGGACCATTTAGCAATGATTACAGTTCATTCAGATTCTCGTGGGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatattccatttttttttttcctcccctagtttttcttttctct-tcgtcttcatcaaatc--catagctggttaaataagtctttattaaagaaaagg
 || ||||| |||||  | |||||||| || |||||  |   ||||||||||  ||||||||||||||| ||||||||||| |||| | | || ||||||||   ||  | || |    |    |  |   || ||| |   |      |       || |  |   ||||  || | ||  |     |         |    
CGCACTTCTTGACCACATGGCAATGATCACGGTTCAGACTTCTTCTCGTGGGGTCTTTGATTGCAAGCCTCTTGGTTTGATCTGGGCTAAGTTCCCTGAGgtaatattatgcaataaaataacacgccatttattttcttaatggaaagttaatagaattatgttagcatatttgttcaatcatacactcccccgtctac---
















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|110420292|gb|EC986560.1|EC986560
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|27582732|gb|CB005427.1|CB005427
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110712069|gb|EE089270.1|EE089270
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|30129062|gb|CB914401.1|CB914401
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110362932|gb|EC926494.1|EC926494
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110398569|gb|EC965022.1|EC965022
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110380341|gb|EC945597.1|EC945597
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110731285|gb|EE105571.1|EE105571
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|110393671|gb|EC959079.1|EC959079
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
EST: gi|294966960|gb|GW839835.1|GW839835
EST:     GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAG                         TTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT
genomic: GGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatatt ... atttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCTTCTGGACCATTTAGCAATGATTACAGTTCATTCAGATTCTCGTGGGCCCTTTGATTGCAAGCCACTTGGTTTGATATGGGGTCAATTTCCTGAGgtctgatattccatttttttttttcctcccctagtttttcttttctcttcgtcttcatcaaatccatagctggttaaataagtctttattaaagaaaagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa