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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttcttctatctctgttatatttctttgtttaatgtcacagaattagttatttcctaggtgacacttagacaactcaaaacacttgaagttgct...

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 23
TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttcttctatctctgttatatt--------------tctttgtttaatgtcacagaattagttatttcctaggtgacacttagacaactcaaaacacttgaagttgct-------------------
|||||||||||||||||||||| || ||||||||||| || ||||| || ||  |||||||||  ||||||| ||||||||||||  | || ||| | | |||||| || |  ||||  |||| | ||              ||  |    ||| |   |  | |  || |||  | | |   |  ||  |  || |     ||   | |   |                   
TGTTGATGAGTGATTCACTTGGGGGTAATGCCAAAACCCTCATGTTTGTGAATGTATCTCCAGTAGAATCAAGCTTGGATGAAACACATAACTCTCTAATgtatgt-ttttcttatccttgttttcttgaactctacaaagttcacttccaaatcttttaatagttttttttttttggctagtatgtattct-cttagtgttctaataatctttatattttatgctaattcag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 23
TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttct-tctatctctgttatatttctttgtttaatgtcacaga-attagttatttcctaggtgacact-tagacaactcaaaacac-ttgaagttgct-------------------------
||||||||||||||||||||||||| |||||||||||||| ||||| || ||  | ||||| || |||||||| ||||| || ||  | || ||| | | ||||||  | | ||  | ||| | ||  |  ||  |||| | |    || ||     ||   ||||    | |   |   ||||  |||    ||    ||| |                         
TGTTGATGAGTGATTCACTTGGTGGTAATGCCAAAACTCTCATGTTTGTGAATGTTTCTCCTGCAGAATCAAATTTGGACGAGACAAATAACTCTCTTATgtatgttctttgtcgttttctttcattataattattttattattgttgagatctcacatcaactagagatctcaacaattaacttgaaaagtgtttctattgttctaacacaattcctctgttatttag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 26
TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttcttctatctctgttatatttctttgttta-atgtcacag-aattagt--tatttcctaggtgacacttagacaactcaaaacacttgaagttgct----------------------------------------------------------------------
|||| |||||||||||||||||||| |||||||||||||| ||||| || ||  |  ||||  | |||||||| |||||||| ||  | || ||| | | ||||||  | |  ||| |   ||   | |   |||| | || |||||  || |||   |||  || | ||| |  |      | |  |   || | |  ||  |                                                                      
TGTTAATGAGTGATTCACTTGGTGGTAATGCCAAAACTCTCATGTTTGTGAATGTTGCTCCCACAGAATCAAATTTGGATGAGACAAATAACTCTCTCATgtatgttctttcttattttctttcattattaatgttgagatttcacatcaactagcgatataaccaatgtgtctttgtagggattacattgaccttatcttttttatgtgagatctaaacaattgacttgaaagtgtctctcttgttctaacatcattcatctttgttatttag

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 23
TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttcttctatctctgttatattt---cttt----gtttaatgtcacagaattagttattt--cctaggtgacacttagacaactcaaaacacttgaagttgct---------------------
||||||||||||||||||| || || |||||||||||||| ||||| || ||  ||||||| |  || |||| ||||||||| ||  | || ||| | | ||||||  |  ||  | | |  | || ||   ||      ||||| | ||| |   ||  |  |||    | | | | |  | |    |||  |    |  ||    ||                     
TGTTGATGAGTGATTCACTAGGGGGTAATGCCAAAACTCTCATGTTTGTGAATGTATCTCCGGTAGAGTCAAGCTTGGATGAGACGCATAACTCTCTAATgtatgttcttctccttgttttctttacttgaactccaaaagtttactttcaaatctttcatagttttatttggctaatatatggtattctcttagtgttctaataatctttatattttatgctaatttag

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|30252243|gb|CB969794.1|CB969794
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|71880280|gb|DT029335.1|DT029335
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTA
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTA
EST: gi|30252337|gb|CB969888.1|CB969888
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATTTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|110361383|gb|EC924851.1|EC924851
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|110422405|gb|EC988728.1|EC988728
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|30252330|gb|CB969881.1|CB969881
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|30252250|gb|CB969801.1|CB969801
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
EST: gi|110419545|gb|EC985782.1|EC985782
EST:     AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGAC                         GTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC
genomic: AACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttc ... tttttatcagGTATGCATCTAGGGTCCGGTCAATTGTAAATGATGCAAGCAAAAATGTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGATGAGTGATTCACTTGGTGGCAATGCCAAAACTCTTATGTTCGTAAACATATCTCCAGCTGAATCAAACTTGGATGAAACTTACAATTCTTTGACgtatgtgttcttctatctctgttatatttctttgtttaatgtcacagaattagttatttcctaggtgacacttagacaactcaaaacacttgaagttgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaca