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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcattgtttttgttgattaatttttcctgtgtttttaattgttaaagtcaaattctatcttcaagtggaatgatgatgtcttgcatatgcttttt...

Basic information

species Vitis vinifera
transcript Vv16s0039g02410.t01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 21
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcat-tgtttttgttgattaatttttcctgtgtttttaattgttaaagtcaaattctatcttcaagtggaatgatgatgtcttgcatatgcttttt
||| || |||||  | || ||||| |||||||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||||||  | ||||| |||||||   || |  | ||  || ||       |  ||| ||  | | || |||      ||||   |||   |     |||||       | | ||   || 
TGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCATTCAAATTTATAATGTCCGTGTTGACGAGgtgagtgatattctcttaatggttctcaccgcaagtgattaaactagtcaaataatgtttctcatttcctcttaccagatgaatcagatcttgtgagatt-

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt--gtttttgttgattaattt---ttcctgtgtttttaattgttaaagtcaaattctatcttcaagt---ggaatgatgatgtcttgcatatgcttttt----------------------
 ||||| |||||| | || || ||||| ||||| || ||||||||||| || |||||||| ||||| |||||||| || ||||||||| | || ||||||||     ||   ||  |||     ||| ||    |  |||| |||       |   ||  |    ||| |    ||      || |   |||| |  ||| ||||  |                      
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 21
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt-----gtttttgttgattaatttttcctg--tgtttttaattgttaaagtcaaattctatcttcaagtg-gaatgatgatgtcttgcatatgcttttt-----------
 ||||| |||||| | || |||||||| ||||| || || |||||||||||||||||||||||||| ||||| || || ||||||||| | || ||||||||     |       ||| ||  |   | || |  | |   | | || | ||||    ||||  || |||  |  |    |||| ||| || ||       ||||| |           
AGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAATACAGATTTATAATGTTCGTGTAGATGAGgtattttaccaggccgttctttctttgtgatctcccgtacctatgttgatttgtattcgtcagtttgtattctagatcccgaataatg-tgcctaattagagctttctgctgttggcag

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|71879756|gb|DT028811.1|DT028811
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71878707|gb|DT027762.1|DT027762
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71880708|gb|DT029763.1|DT029763
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71879963|gb|DT029018.1|DT029018
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71863790|gb|DT012845.1|DT012845
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAG                         GTCAAAACAAAACTCAAGG
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGG
EST: gi|71879582|gb|DT028637.1|DT028637
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71879455|gb|DT028510.1|DT028510
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71879339|gb|DT028394.1|DT028394
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71878846|gb|DT027901.1|DT027901
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71880267|gb|DT029322.1|DT029322
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71880607|gb|DT029662.1|DT029662
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71878134|gb|DT027189.1|DT027189
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71879171|gb|DT028226.1|DT028226
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71881027|gb|DT030082.1|DT030082
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
EST: gi|71881083|gb|DT030138.1|DT030138
EST:     TAGGAATGGAGGATTCTACAATTCAAATATATAATGTCAGAGTTGATGAG                         GTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT
genomic: TAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcatt ... atgttggcagGTCAAAACAAAACTCAAGGGTCACCAGAAACGAGTAACCGGACTTGCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAATTCAAATATATAATGTTAGAGTTGATGAGgtgaagcattgtttttgttgattaatttttcctgtgtttttaattgttaaagtcaaattctatcttcaagtggaatgatgatgtcttgcatatgcttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagtcaa