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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag

Basic information

species Vitis vinifera
transcript Vv15s0046g02420.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 5'ss of exon 2
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca--tgatcagacccaatcacttctcatctcatcatttatctgtgaatctgcct-tgtattgat-ttcattcttttgttgttcccttcag--
||| ||||| ||||||||||||||||| |||||||||||||| || ||||| || || || ||||||||||||||||| |  |||||||||||||||   || || |  |  | |    | |||| | |||     ||| | |  | |      || |   | | |||  || |  ||   | | |   |   |  |   
TCACCTGGCCACCATCCCCATCACCGGCACCGGCATCAACCCAGCGAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGGCCATGCCTGGGATGACCATgtgagtttaaattcactgaaaccaacccctttctccctccttacatgtagaaatatatatatatatatatatatatatatatatatatatatatatatat

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 5'ss of exon 2
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctca----tctcatcattta---tctgtgaatctgccttgtattgattt-cattcttttgttgttcccttcag
 || ||||| ||||||||||||||||| || ||||||||||| || ||||| || || || ||||||||||||||||  || ||||||||| |||||   || |||  | |       |    |  || |||     ||||| || ||     || | |   |  |   ||||  |   ||     ||| |  ||  | |  
CCACCTGGCCACCATCCCCATCACCGGTACTGGCATCAACCCAGCCAGGAGCCTTGGCGCTGCCATCATCTACAACAAGGACCATGCCTGGAATGACCATgtgagcaacctttcttctctttttacctactcgccgttctcagcaattggttcctcttacattatcagatattagtcagcacatcattgataatcgatac--

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g57720.1 (Oryza sativa), 5'ss of exon 1
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcattta-tctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag-----
 || || || ||||||||||||||||| |||||||||||||| ||  | || || || ||||||||| |||| ||| | |  || || ||| | |||   ||| ||  |        |   |||   |||||| ||  | |  || ||  |  ||| |      |   | |     | |      |||  ||        
CCACCTCGCCACCATCCCCATCACCGGCACCGGCATCAACCCCGCCCGCAGCCTCGGCGCCGCCATCGTCTATAACCGCGCCCACGCATGGCACGACCACgtatgcaaccaaccattatttaatgctttctcaactacttagctactccatccatccgataaaaaaccaatcggaacgtgacacattctattattatgta

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G392975_T02 (Zea mays), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGAC-ATG-
 || || || ||||||||||||||||| |||||||||||||| |||||||| || || |||||||||||||||||| | || ||||| |||   ||| |||   ||  |  |     ||    ||  |  |  |  || ||    |  | | |||   |    || | | |     || | |  |||   ||| | ||     
CCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATCTACAACCGGGATCATGCGTGGAGCGACCATgtgagtgggaactgctctcgattcctctggcaccaaatttcggtttccaacagtgtggtaccactcgcactcg---cagtgtagtgtgtctccatccaaatac

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G392975_T03 (Zea mays), 5'ss of exon 3
-------------------------------TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag
                                || || || ||||||||||||||||| |||||||||||||| |||||||| || || |||||||||||||||||| | || ||||| |||   |||   || ||      || | |  |      | |||     ||   ||    |   || | |  | |||    |  ||                     
CACTGCCAATTGGGTTCGCGGTGTTCCTGGTCCACCTTGCCACCATCCCCATCACCGGCACCGGCATCAACCCGGCTAGGAGCCTTGGCGCCGCCATCATctacaaccgggatcatgcgtggagcgaccatgtgagt---gggaactgctctcgattcctctggcaccaaatttcggtttccaa-cagtgtggtaccactcgca---------------------

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G081843_T01 (Zea mays), 5'ss of exon 1
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgat--cagacccaatcacttctcatctcatcatttatctgtgaatc--tgccttgtattgatttcattcttttgttgttcccttcag
 || ||||| ||||||||||||||||| |||||||||||||| ||  | || || || ||||||||| ||||||||||    || || ||| | |||   || || | |||  |  |     | |||  |     ||||||  |    | | || |   || ||    |||  ||    || || || || |      
GCACCTGGCGACCATCCCCATCACCGGCACCGGCATCAACCCCGCGCGCAGCCTCGGCGCCGCCATCGTCTACAACAGGTCCCACGCATGGAACGACCACgtgagtttcattctggccatgtcgatcgatcgaattctcatgctgcggc-gcgagttcatgactgaccttggatttgaactattattattgcag----

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AC209208.3_FGT002 (Zea mays), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaag--------ctccatgatcagacccaatca-cttctcatctcat-catttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag
 || || || ||||||||||| || || || ||||||||||| |||||||| || || || ||||||||||||||||| || || |||||| | |||   || ||        |||     ||    | || || |||  ||| || | || ||   |   | || ||  |||| ||  | ||| |   | |    |       
CCACCTTGCCACCATCCCCATTACTGGCACTGGCATCAACCCAGCTAGGAGCCTTGGCGCTGCCATCATCTACAACAGGGATCACGCCTGGAACGACCATgtgagtggaactactctcgattcccctctaaccaactttccatttcctacagtttggtaccactc-gcagtgtaatgtctccatccaaatatcagacatcc---

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G174807_T01 (Zea mays), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttgtattgatttcattcttttgtt-gttcccttcag-------
 || ||||| |||||||| |||||||| |||||||||||||| ||  |||| || || |||||| | || ||||||    | ||||| |||| ||||   || ||    |  | ||       ||     || | |  | |  ||  |      ||       |   |    ||| ||| | |   |     |||       
CCACCTGGCCACCATCCCTATCACCGGCACCGGCATCAACCCCGCGCGGAGCCTTGGCGCCGCCGTAATTTACAACCAGCACCATGCGTGGGCTGACCACgtgagtggaa--aacaactttcttctaccttcgtgttgttaactagtttcactgctttagcaaaaaaaaaaaattgtttagctcactgttaacagtagtatg

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G37730.1 (Glycine max), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttg---tattgatttcattcttttgttgttcccttcag---
 ||  |||| ||||| |||||||| ||||| ||||| ||||| ||||||||||| || || |||||||||||||||||||| ||||| |||||||||   ||| | | | |  |        |  ||||   || |  | |  ||| |    ||  || | |    ||    |  ||  || | ||| |   |  |    
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttcttacttcctttttaagactttaaattttgttacatatattcccattagcataggaaaataaggtaaatagttatattgatttttataataa

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G01860.1 (Glycine max), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaa----tcacttctcatctcatcatttatctgtgaatctgcct---tgtattgatttcattcttttgttgttccctt-cag
 ||  |||| ||||| |||||||| ||||| ||||| ||||| ||||||||||| || || |||||||||||||||||||| ||||| |||||||||   ||| | |   |  | ||||   |    |   |||  || |   ||||    |  |||      |   |   || |||  ||| | || |  ||  ||| | |
CCACTTGGCTACCATTCCCATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTCGGAGCTGCCATCATCTACAACAGAGACCATGCATGGGATGACCAAgtatgtttttt--tgagacttgaatttttgtttcatatattcccattagcataggaaataatgtaaatagttttattgaattttattataattatcttaccg

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G02530.1 (Glycine max), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttct-catctcatcatttatctgtgaatctgccttgtattgatttcattcttttg-ttgttcccttcag
 ||  |||||||||| || ||||| ||||| ||||| ||||| ||||||||||| || || || || || ||||||||||| ||||| |||||||||   |||       |   ||   ||  |||||| |    ||| |  ||| |   ||||  || |||   || | |   |  ||||  ||||  | | |||
CCACTTGGCAACCATTCCAATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACAGAGACCATGCTTGGGATGACCATgta-------tatacatgtcctttcacttatgtgcctctttgttt-tgcatgaaagtgactttatttaactgtttaattttaattgtggcttacag

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGAC-ATG-
 ||  |||| ||||| || ||||| ||||| ||||| ||||| ||||||||||| || || || || || |||||| |||| ||||| ||||||||| |||  || |  |  | |          ||  |  |  ||| |  | | |  | |  | | |  |  | |||||||     |   |             
CCACTTGGCTACCATTCCTATCACAGGAACTGGCATTAACCCAGCTAGGAGTCTTGGTGCTGCTATAATATACAACCGAGACCATGCTTGGGATGACCATgtatatgtcctttcacttatgtgcctctttgtttttcttacaagtgacttatttaacggtttaattttgattttggcttacag-------------

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S1_535V6.2 (Physcomitrella patens), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCAT---GCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttgtattgatttcattcttttgt-tgttcccttcag--------------------------------------------------------------
     |||| ||||| |||||||||||||| ||||||||||| ||  | ||||| || || ||  |  |||  |||| | || |    || ||||  ||    || || || |   |  |   |     ||| || | |  ||    |      | |     |    |       || ||| ||  | || |  ||||                                                              
---CTTGGCCACCATTCCCATCACCGGAACTGGCATCAACCCCGCCCGTAGTCTAGGTGCTGCTGTTGTCTTTAACAAACAGAACAACGCTTGGGCCGATCACgtgagttcaagcttttgcttccccaccttatcctatgctcgccgaatgcaaattgcaaatcacgtcagggatatgcttatgaatattgctctcagtattagttgtcaggctcatgtcggacgggctttgatctctgttttttttggtgcttttgcag

upper sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 3
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCA---TGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcat--ctcatcatttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag----------------------------------------------------------------------
   | |||| ||||| |||||||||||||| ||||| ||||||||  | |||||||| || |||| |||||||||||   ||||   ||||||||  ||    || || | |||  ||   | | |   || || |    |||   || |  |  | |  |  | | |   |||||  ||  | ||  ||||  |  ||                                                                      
---TTTGGCCACCATTCCCATCACCGGAACTGGCATTAACCCTGCACGTAGTCTGGGCGCGGCCACCATCTACAACACGCAGCACAATGCCTGGGCCGATCACgtgagttgcattctcttccaccactcctgctgaaaattcaaggttaaggttaggacttatcgtctggagatttattttctatgg-gttcggtctagaaacgaatggttatcaggcacaatatgaaggagctgtaacctctctgaaatgttgattgtgctgctgcag

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|110698200|gb|EE075479.1|EE075479
EST:     GTCTGGGGGCCGCCATCGTCTACAACAAAGAGCATGCCTGGGATGACATG                         TGGATTTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTG
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTT-CTGGGTTGGACCCTTCATTGGAGCTGCTCTTG
EST: gi|87585869|gb|DY474409.1|DY474409
EST:     GTCTGGGGGCCGCCATCGTCTACAACAAAGAGCATGCCTGGGATGACATG                         TGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC
EST: gi|110702789|gb|EE079065.1|EE079065
EST:     GTCTGGGGGCCGCCATCGTCTACCACAAAGAGCATGCCTGGGATGACATG                         TGGATTTTCTGGG
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTTCTGGG
EST: gi|110357108|gb|EC920423.1|EC920423
EST:     GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATG                         TGGATTTTCTG
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTTCTG
EST: gi|34544388|gb|CF512620.1|CF512620
EST:     GTCTGGGGGCCGCCATCGTCTACAACAAAGAGCATGCCTGGGATGACATG                         TGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC
EST: gi|34546377|gb|CF514609.1|CF514609
EST:     GTCTGGGGGCCGCCATCGTCTACAACAAAGAGCATGCCTGGGATGACATG                         TGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC
genomic: GTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctcca ... ttcccttcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTGCTCTTGCTGCCTTGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCTGGCAACCATCCCCATCACCGGAACCGGCATCAACCCTGCTAGGAGTCTGGGGGCCGCCATCATCTACAACAGAGAGCATGCCTGGGATGACATGgtaagctccatgatcagacccaatcacttctcatctcatcatttatctgtgaatctgccttgtattgatttcattcttttgttgttcccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA