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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAATAACAAGAGTCCGGGAGATGTTCCTGGAAATGTCTTGCTGGTAACAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctttttgcttggaagctattttcatttgggctctctattagatgtttcgaatcctcatattgtctagctgatatagtttgcaaaaacgagtta...

Basic information

species Vitis vinifera
transcript Vv14s0108g01030.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G37080.1 (Glycine max), 5'ss of exon 2
TGTCAATAACAAGAGTCCGGGAGATGTTCCTGGAAATGTCTTGCTGGTAACAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctttttgcttggaagctattttcatttgggctctctattagatgt-ttcgaatcctcatattgtctagctgatatagtttgcaaaa-acgagtta-
|||||| ||||| || || |||||| ||||||||||||||||||||||||| || || ||||| |||||||| ||||||||||| |||||||| || ||||||||||    |   ||  |    |||     |  || |  || ||   ||| |  |  |   |||  |   |   || |    |  |       |  |||  
TGTCAACAACAAAAGCCCTGGAGATATTCCTGGAAATGTCTTGCTGGTAACTATTGAAGGTGTGGAAGCTGGGGATGTGAGCATTGATGTTATCCATTTGgtaagtgtgagtaagttttatttcatt---gctctggtttgctgttgtgtgtatgtgtttttgcatgcttcttgtttggttagatgcgtggtgtgcatgtttt

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G49580.1 (Glycine max), 5'ss of exon 2
TGTCAATAACAAGAGTCCGGGAGATGTTCCTGGAAATGTCTTGCTGGTAACAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctttttgcttggaagctattttcatttgggctctctattagatgt-ttcgaatcctcatattgtctagctgat---atagtttgcaaaaacgagtta--
 ||||| ||||| || || |||||| ||||||||||||||||||||||||| || || ||||| |||||||| ||||||||||| |||||||| || |||||||||||   |   ||      | |  |   |  || || || ||   ||| |  |  |   |||  | ||||  || |   ||   | |   | | |  |||  
-GTCAACAACAAAAGCCCTGGAGATATTCCTGGAAATGTCTTGCTGGTAACTATTGAAGGTGTGGAAGCTGGGGATGTGAGCATTGATGTTATCCATTTGGtaagtgcgactcagttt----ttttcattgctctggttcactgttgtgtgtatgtgtttttgcatgct-tctatttggttagatgcgtggtgtacatgttttaag

upper sequence: Vv14s0108g01030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 5'ss of exon 2
TGTCAATAACAAGAGTCCGGGAGATGTTCCTGGAAATGTCTTGCTGGTAACAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctttttgcttggaagctattttcatttgggctctctattagatgtttcgaatcctcatattgtctagc-tgatatagtttgcaaaaacgagtta----
|||||  |  ||||   | || |||||| |  | ||||||||||||||||| || ||||| ||||||||||||||||| ||||| || ||  | ||| | ||||||  || |  ||   ||   | | |  | | | ||     |||   ||    || | |   || |    |  |||||  |  | | |    |   |     
TGTCACCAGTAAGAACTCTGGGGATGTTGCAAGCAATGTCTTGCTGGTAACGATTGAGGGCGTAGAAGCTGGCGATGTCAGCATTGACGTGTTACACCTTgtaagttattctatctc--aattaactattgtatagcctaaaattta---gtcgaaaaacgtggcatggagcggagtgatagggaatacgagtctgttctgctcc

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|351026199|gb|FQ428211.1|FQ428211
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|351019653|gb|FQ439470.1|FQ439470
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|351017354|gb|FQ435706.1|FQ435706
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|351023752|gb|FQ448303.1|FQ448303
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|351016914|gb|FQ424341.1|FQ424341
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|349818542|gb|FQ403177.1|FQ403177
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACCTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|161716509|gb|FC066200.1|FC066200
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
EST: gi|351024488|gb|FQ426297.1|FQ426297
EST:     CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTG                         GTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT
genomic: CAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctt ... tttattacagGTGTTCTCTGCTTTTGGATTTGTGCACAAAATTGCTACATTTGAAAAGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAATAACAAGAGTCCGGGAGATGTTCCTGGAAATGTCTTGCTGGTAACAATCGAGGGTGTAGAAGCTGGCGATGTGAGCATAGATGTTATTCACTTGgtaagtgctttttgcttggaagctattttcatttgggctctctattagatgtttcgaatcctcatattgtctagctgatatagtttgcaaaaacgagtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaaa