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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct...

Basic information

species Vitis vinifera
transcript Vv02s0025g01410.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgtt-ttacctgaatttat-------cactcctttttttcccctgattttggttctctctca-gtttcattgtgta-tgcctct---------------------------------------------------------
 || || ||||| ||||| || ||||||||||||||||||||||| || || || || || ||||| |||||||||||||||||||||| ||| || |||||||    || |  ||  | |   | |  |  | | | |||||||       || |  ||||       || | |      |  || | |  |||||   |  ||  |||                                                         
CATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAATTTGGAGAACATTTATGGTCTTGTTTCTGCTATAGATTCGgtatatggct-atctgctttaaagttctctgctccttaaatttattctgcgacattgtttttgcctttttggtatcataaatgactgatgggtcattaccttctgtttctgctaaaacaatttgaaaaactttcctctgttttttttttttttgaacatctgttcag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatg-cctctcaaatgtgtcatcat---------acgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcatt-gtgtatgcctct--
 || || |||||||||||||| |||||||| || ||||||||||| || || || ||||| ||||| ||||| |  ||||  | | ||| | |||| ||||||    ||   ||    |   ||||         || ||||  |     | | |  || |   |||||     ||    | ||  |||    | ||| |   ||  |||   
CATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAATTTGGAGAACATATTCGGTCAAGCTCCTGGTGTTGATTCGgtacaatctgataacctagctttcatttgctcaaaaccttttttccattataaccgatcttacgtttccatatgttgacatgctgactcgccgttatttgacaatctctccag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgt-atgcctct----------------------------------------------------------
 || ||||| || ||||| |||||||| |||||||| || ||||| || || ||||| || ||||| ||  |||||||||||||||||| ||| |||||||||||    | |       |||  ||  |||| |  |  |||   | |  | | |   |  |||  |  |        ||| || ||| | | | || | |                                                          
CATAGACCGTAAAAAGAATATATTCAAACTTTCACAGGGTGAATATGTGGCAGTTGAAAATTTGGAGAATGTTTATGGTCTTGTTTCTGCTATAGACTCGgtatg----taatggacaacatttta-atttttctggtcttttcaaattttctgtagtctatgaaatgcgaataaaaccagattgattttcttaggcttatgtcctagttgttctgctgaaggaacatgaattggcttcaatctttttgaattttttag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattt--tggttc-tctctcagtttcattgtgtatgcctct--
 || ||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||||  |||| ||||| | |||||    | ||| | |||| ||||||   |||  ||  || |     |||    |    |  ||   ||     |  || |   | |||   |  | | ||||| ||| | |  |  ||   ||    
CATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAATCTGGAGAACATCTTTGGTCAAACTCCTGCTGTTGATTCGgtacagctcaaaacagtcttcatctacacagtctaagtgttctgcagcaaatggttacaaataattccataatccatctctaagtctaaacg-atacatcttcag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA05G36910.1 (Glycine max), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtc---atcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct--------------------------------------------------------------------------
||| || || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||| |||| || ||||||| ||  | ||||  | |||| || ||||| ||    ||    ||    | |  |   ||| |||  || || |    |  | |  |      |||||||  ||   |   |  |     | |  |                                                                            
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAACCTGGAGAATATTTATGTTCAAGCTTCTTCTGTTGAATCTgtatgtcttgtgaacccttctcttttaatcaacttatctgccttcattatgaatgatat--caaaaggtttggtttactgcaaagatagtaacaaaggttttagtttcagcttcatttcatgagcagataatgttccgtgatatgttgatattacttcttttccaactctatttcag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct
||| || || |||||||| ||||| |||||||||||||||||||| ||||| || || ||| |||| || ||||| ||||  ||||||  |||||| || ||||| |             ||| ||    || |     |||     ||||   ||       ||||     |    |||  ||       || |     
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgactcctgagaatcctattccttccaatggttttggtgtcctaacttgtagtaaatttattaccaaaatcaaattggaaaaataagtagaa

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagttt-cattgtgtatgcctct-
||| || || |||||||| ||||| |||||||||||||||||||| ||||| || || ||| |||| || ||||| ||||  ||||||  |||||| || ||||| |     |||       | | |  | | ||  | |  ||   | | | ||   |  |  |  || ||   |    ||   |||| ||||   |  | 
TATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAACCTGGAGAATATTTACGGTCAAGTTTCTTCTATTGAATCTgtatgtcctgagaatcctattccttccaatgtcccccagt--attggtgcatgttgatctatattagtgatttagtgaatgtccacattctgtagttcagta

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT1G64400.1 (Arabidopsis thaliana), 5'ss of exon 14
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct
 |||||||| ||||||||||| || || || || |||||||||||||||||||||||||||||||| ||||| ||  ||| |||  | |  ||||| |||||||   |   |||| |  | || || ||      |  ||  | |    ||  |  ||   | |         | |  |||                   
CATCGACCGTAAGAAGAACATCTTTAAACTGTCTCAAGGAGAATACGTTGCCGTTGAGAACTTGGAGAACATATACAGTCATGTCGCCGCCATTGAATCGgtattagttgaaaatataac-tcttaagtaaccgttacataaaacttagctaatgatctgttaa-----aacattttgcag-------------------

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 5'ss of exon 13
--------------------------------------------------------------TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATAC--GTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtg----tcatca--tacgttttacctgaatttatcact--cctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct--------------------
                                                               |||||||||||||||||||| ||||||||    || || |  ||   | |||   ||      ||      |||    |      ||    | |  || |     ||  | |||  | |    ||  ||   |||  |  |      |  | |||  | || | || ||||||   | |  |||| |      | | |     || |||                    
GCGGACGGCTTCTTCCACACGGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCAGGgtgcgtaatggctgcgtatgcatggctgccgcgaattaggagctcgacttgccgtgtatacactccgggcggcacaagcggggagctcggcaggcacgagtggcgatgtgtgctgacttgcattgtgttgccctgacactcggcctctgtgtcaaccctggccccggcgtctgccattgccgtgtgccccag

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S113_124V6.1 (Physcomitrella patens), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttt-tacctgaatttatcactccttt---ttttcccctgattttggttctctct-cagtttcattgtgtatgcctct
||||||| | ||||| ||||| || ||  | |||||||||||||||||||| || |||||| | |||| |||||||||||    |     | | ||   ||||    | ||     | |    |   | |   | |  ||| |||||    |      ||  | ||  ||| || | |   | || | | ||  | |        
TATCGACAGGAAGAAAAACATTTTTAAATTGTCACAAGGAGAATACGTTGCAGTCGAGAACCTTGAAAGCATTTATGGTCAATGTGAACTTGTGGATCAGgtactagtgtcgtgcatttatctaggggctagcaacaaaatctatcaggtgtacgagcttatctcttctttgggctttaattgcaatgttatgatttggt-----

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcag-tttcattgtgtatgcctct----------
||| || |||||||||||||| ||||||||||| ||||||||||||||||| || || ||| | |||||  | ||   |      ||   | ||||  |||||||          |  |||   |||| ||   |||  || || |     || || |  |    |    | || |  ||| ||||  | |       ||           
TATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAACCTTGAAAATGTGTACAATGAGTCCTCCTCTGTTGATGCGgtatga---------gcatcactttacgattctgctg--ttcataatctagttcttgcaaccacatgcactgctttagcagatttcgatctacccatttcggtactaggtt

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: EFJ25426 (Selaginella moellendorffii), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct
 || ||| | ||||||||||| ||||| || || ||||| |||||||| || || ||||||||||||||||| || || |      |     | || |||||  |   |       ||  | |||     || ||   ||| |   || |  |||    || |                                     
CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc-----atgcgagcatcgagattgccaatattaactgctgccctttcgatccag-------------------------------------

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: EFJ23443 (Selaginella moellendorffii), 5'ss of exon 16
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct
 || ||| | ||||||||||| ||||| || || ||||| |||||||| || || ||||||||||||||||| || || |      |     | || |||||  |   |       ||  | |||     || ||   ||| |   ||  | |||    || |                                     
CATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAACTTGGAAAACATCTACGGCCAATGCCCGACCTTCGATTCGgttagttgcc-----atgcgagcatcgagattgccaatattaactgctgatctttcgatccag-------------------------------------

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|30125801|gb|CB911140.1|CB911140
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|110375957|gb|EC940989.1|EC940989
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|27580341|gb|CB003036.1|CB003036
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|349816864|gb|FQ399732.1|FQ399732
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCCTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|352781554|gb|FQ468398.1|FQ468398
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|351053855|gb|FQ441621.1|FQ441621
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|32245315|gb|CD711134.1|CD711134
EST:     AAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: AAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
EST: gi|27755362|gb|CB036117.1|CB036117
EST:     CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCG                         ATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC
genomic: CCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctct ... ttaattgcagATATGGATTTACGGCAACAGCTTTGAGTCCTTCCTTGTTGCTGTTGCTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAACTTGGAAAACATTTATGGTCTTGTTTCTGATATTGACTCGgtatgcctctcaaatgtgtcatcatacgttttacctgaatttatcactcctttttttcccctgattttggttctctctcagtttcattgtgtatgcctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc