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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAACTCGACGTACCGTTCCAGTTAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactcaatagtgggtttttttttggcag

Basic information

species Vitis vinifera
transcript Vv13s0019g05390.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g57750.2 (Oryza sativa), 5'ss of exon 3
CAAGAACTCGACGTACCGTTCCAGT--TAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtac-ttga---ttactgttagaaggcccctt---cacatcttttagttgccttttgctctggt---aatttactcaatagtgggtttttttttggcag
     ||| ||| |   |  ||| |  |||||    |||| |||||  ||| ||||||||||| ||||| ||||| |||||||| |||||| | || ||||||||  ||||   | | |  |||||   |       || ||  |||  |||   ||   |||| |   | | |  |||||       ||| |  |  |||
-CTCCACTTGACATGG-GCCCCATTCCTAGAACTGAAAATAGATTCATCCCGCCAGATGATGACAATGTGTACAGCATGGAACTGAGAGAATTGCTTAGCAGgtatattgaccttcagtactagaatttcttccaaacatattcttttattgatattaaatctgttcttattctgatcaatgaccacgtttgtactttcag

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G33300.1 (Glycine max), 5'ss of exon 5
CAAGAACTCGACGTACCGTTCCAGTTAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactcaatagtgggtttttttttggcag-------------
| || | ||| |||   |||||  | |||||| | ||| |||| || ||||| |||||||||||||||||||||||||| || ||||||||||| |||||||| ||  || || ||  |      | |||||  |     || |    || |  | | |||||  | |  ||       | ||||  |              
CGAGGAATCGCCGTGGGGTTCCCATAAGAAGATTCAATAGATTTCATCCACCTGATGATGATAATGTATACAGTATGGAGCTTAGAGAACTTCTGAGCAGgtaattctttccttttgaatctttgcctcacagatggc--tttcagcctgtttggcttatttatcccactgtcaacaggtgtttgagaaaaggaaataaaag

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G34240.1 (Glycine max), 5'ss of exon 6
CAAGAACTCGACGTACCGTTCCAGTTAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactcaatagtgggtttttttttggcag-------------
|||| | ||| |||   |||||  | |||||  | ||| |||| || ||||| |||||||||||||||||||||||||| || ||||||||||| |||||||| ||  ||  | ||  |      | || ||  |     |   | | |  |  | | |||||  | |  ||       | ||||| |              
CAAGGAATCGCCGTGGGGTTCCTATAAGAAGGTTCAATAGATTTCATCCACCTGATGATGATAATGTATACAGTATGGAGCTTAGAGAACTTCTGAGCAGgtaattctttctttttgaatctttgcctcgcagatggctttcagcctct--ttggcttatttatcccaatgtcaacaggtgtttgggaataggaaataaaag

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G04460.2 (Arabidopsis thaliana), 5'ss of exon 4
CAAGAACTCGACGTACCGTTCCAGTTAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgattactgttagaaggccccttcaca----------tcttttagttgccttttgctctggt--------aatttac--tcaatagtgggtttttttttggcag
 ||| | ||| |||   || |   | |||||| ||||| | ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || || ||||||||||  |    | ||||        || |||          | |||| |||   | || |  || |         ||| |   |   ||  |  |||| | || ||||
TAAGGAGTCGCCGTGTAGTACAGTTGAGAAGATTAAATAGGTTCCATCCACCTGAGGATGACAATGTTTACAGCATGGAACTCAGGGAGCTCCTAAGCAGgtactaaaaaggttttagccacatttttgacaaaggtggatttgttttcgttctttattaccttgatttctgtgagattgatgatttctaccgtcttttctgtttgcag

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|110362870|gb|EC926428.1|EC926428
EST:     CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
EST: gi|30302439|gb|CB979233.1|CB979233
EST:     CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
EST: gi|110697361|gb|EE074284.1|EE074284
EST:     TGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: TGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
EST: gi|110722021|gb|EE097887.1|EE097887
EST:     CCAGATGATGATAATGTATACAGTATGGAACTCATAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
EST: gi|33404749|gb|CF210376.1|CF210376
EST:     CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
EST: gi|30136916|gb|CB922254.1|CB922254
EST:     CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAG                         GAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA
genomic: CCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgatt ... tttttggcagGAGAAGTGTCTCAAATCTTCTACGTAGTGGTTTTCGTGAGAGTTTAGACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAACTCGACGTACCGTTCCAGTTAGAAGAATAAATCGATTCCACCCACCAGATGATGATAATGTATACAGTATGGAACTCAGAGAACTTCTCAGCAGgtacttgattactgttagaaggccccttcacatcttttagttgccttttgctctggtaatttactcaatagtgggtttttttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG