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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc...

Basic information

species Vitis vinifera
transcript Vv00s0551g00030.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgtt---attgaaatgagggttttgttttgggggccaaggatc
 |||||| |  |||| ||| || | || ||||| || ||||||||||| ||||||||||||||||| || ||||| |  ||||| ||||| ||||| ||||||   ||        |   |   | |||   | ||||       | ||||   |    ||  |   |||| |     |||  ||| ||  |   |    || 
GTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGCTCATCTGCAAAGGATGTTGCTAAACAGCTGAAGgtaaagatgtagatacatattttctatctagttattgttcctgtttacctatagtccaactcattacattgcatgtgtggtgatgtcttaag--tctgatat-

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 6
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatact-tgtcttaattttgtcatcccc--ttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc
 |||||| |  |||| ||| || | || ||||| || ||||||||||| ||||||||||||||||| || || || |  ||||| ||||| ||||||||||||  |||        |||||  | | | |    | ||  || |    ||   |     | |||    || ||         ||    ||      ||     
GTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGTTCATCAGCAAAGGATGTTGCTAAACAGCTCAAGgta-aaataaaacaaaactattttctatatctggtctggaatgcagaattatcatgcaagagctacctttaaaccaccaacctt----tgcaatttaacag--

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc
 |||||| |  | || ||| || | || ||||| || ||||||||||| ||||||||||||||||| || ||||| |  ||||| ||||| ||| | ||||||   ||        |   |   | |||   | ||||       | ||||   |   |||  ||       | | ||  || | |       | |    
GTTCTATGTGGTATTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGCTCATCTGCAAAGGATGTTGCTAAACAGTTGAAGgtaaagatgtagatacatattttctatctagttattgttcctgtttacctatagtccagctcataacatttcgtgtgtggtgatgtcttatgtatgatat

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G130987_T04 (Zea mays), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattt-tgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc-------
 || ||| |  |||| ||| || | |||||||| || ||||||||||| ||||||||||| || || || || || |  ||||| |||||||||||||||||| | |         | |||||   ||||  | | |   ||     ||||  ||| |   ||  ||  |  ||  || | |       |   ||    ||       
GTTTTATGTGGTCTTCATGCTGTCAGCCTGTGCTCTGTTCTCAAAGACATGGATTGAAGTTTCCGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacggac-------aaatatacacatctttttatgtaaaattttggtcctg-tttggcattggcataaagctgctggctgtaccagcagctacagtactctgttagg

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc----
 |||||| |  |||||||| || | |||||||| || ||||||||||| ||||||||||| ||||| || || || |  || || ||||||||||| ||||||  |     |     | |  |    || | | |  |||   |   | | |  |||||||  |   |     |   |  |  |||  |     |   |     
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaact-agtatcatcaaagca--catgccgttgtgcttgt-ccgtgcctattttacttctttatgaattcaaatttgcca

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G073498_T02 (Zea mays), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc---
 || ||| |  |||| ||| || | || || || || |||||||| || ||||||||||| ||||| || || || |  ||||| ||||||||||||||||||  ||    || | ||     ||    |||  || |   ||  |||    ||  | |     | ||    || | |  ||||   |    ||   |     
GTTTTATGTGGTCTTCATGCTGTCAGCTTGCGCTCTGTTCTCAAAAACGTGGATTGAAGTTTCTGGTTCATCAGCAAAGGATGTTGCTAAGCAGCTCAAGgtacaaacagctttgcacatctttttatgtaaaattctgggcctgttcg-gtttcagcgtaa--agtgctgcgaagctgctgttacagccagcagctacagta

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgt-tattgaaatgagggttttgttttgggggccaag--gatc----------------
||||||  | | ||| ||| |  |||| ||||| || ||||| ||||| ||||| ||||| || ||||| |||||  ||||||| || |||||||||||||||     | |       | || ||| |      ||||  |    ||          |   || ||||  | ||| ||  ||| | |       ||     ||                
CTTCTACTTGACCTTCATGCTTACTGCTTGTGCGCTCTTCTCCAAGACCTGGATCGAAGTGTCAGGATCTTCTGCGCGAGATGTTGCCAAGCAGCTCAAGgtaattgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacag

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 6
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttg--ggggccaa---ggatc---------------------------------------------------------------------
 |||||  | |  || ||| |  |||| ||||| || ||||| ||||| ||||| ||||| || ||||| |||||  |||| || || |||||||||||||||||  |   |   |  |   | |  ||| |   |   | ||   |   ||  |   |   | |   |||     |||    |  |     |||||   |  |                                                                      
TTTCTACTTGACTTTCATGCTCACTGCTTGTGCTCTCTTCTCCAAGACCTGGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatg--tgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataa--aaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacag

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ11193 (Selaginella moellendorffii), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatg---aattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc
 || || || |  || ||| |  | || || || || || || ||||| |||||||| || ||||| ||||| |||||||||||||| ||||||||   |||| |    |   ||| |  |   ||| |   |  || || | || |   ||     |||                                           
GTTTTACCTCACTTTCATGCTCACGGCATGCGCTCTCTTTTCCAAGACGTGGATTGAGGTTTCTGGTTCCTCGGCTAGAGATGTGGCCAAGCAGCTTCGGgtaagcaagaacttttagctcgtaactcgatct--ttctgacttctctccccgggaattgcag----------------------------------------

upper sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ15673 (Selaginella moellendorffii), 5'ss of exon 5
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatg-aattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc
 || || || |  || ||| |  | || || || || || || ||||| |||||||| || ||||| || || |||||||||||||| ||||||||   |||| | ||    ||  |    ||  |   |   || || | || |   ||     |||                                           
GTTTTACCTCACTTTCATGCTCACGGCATGCGCTCTCTTTTCCAAGACGTGGATTGAGGTTTCTGGTTCGTCGGCTAGAGATGTGGCCAAGCAGCTTCGGgtaagcaagaactttagctcgtaactcgatcttttctgacttctctccccgggaattgcag----------------------------------------

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|71887136|gb|DT036191.1|DT036191
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|30137500|gb|CB922838.1|CB922838
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|110693126|gb|EE069083.1|EE069083
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|110383871|gb|EC948274.1|EC948274
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|30128076|gb|CB913415.1|CB913415
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|71873239|gb|DT022294.1|DT022294
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|30127111|gb|CB912450.1|CB912450
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|71882627|gb|DT031682.1|DT031682
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|110427049|gb|EC993480.1|EC993480
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|77580759|gb|DV219287.1|DV219287
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|110369453|gb|EC933613.1|EC933613
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
EST: gi|34549150|gb|CF517382.1|CF517382
EST:     GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAG                         GAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA
genomic: GGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattc ... gatttttcagGAGCAACAAATGGTGATGCCTGGGCACCGGGAGGCTAACTTGCAGAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgaaa