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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g14240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 1
---gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
       || | |  | |   |  |    ||       |   | |||       |  ||  |||| |       ||   || |||||||| |||||  | || |||||  ||||||| ||||| || || ||||||||||| || || || || || || ||||||||||||||||| ||||||
gtaaagatcccgcattcagcctcttctgttccccccctctccgcgatctgaaaccgtacctgttcttcccggaatgggctg-cagATCCGGTTCATCCTGCTGCAGAATCGGCAGGGGAAGACGCGGCTGGCCAAGTACTACGTCCCGCTCGAGGACTCGGAGAAGCACAAGGTCGAGTACGAG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 1
gta-ctctctcgattatgatgattc-aatcttgattgcgaggagattgagttgctgactc--gttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
||| |   ||||  |  |||    | |||  |   | |||     |   ||| || ||    ||||  |   |   |     ||||||||| |||||  | || |||||| ||||||| || || || || ||||||||||||||  |||| || || ||||||||||||||||| || ||||||
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G052713_T02 (Zea mays), 3'ss of exon 1
gta-ctctctcgattatgatgattc-aatcttgattgcgaggagattgagttgctgactc--gttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG-
||| |   ||||  |  |||    | |||  |   | |||     |   ||| || ||    ||||  |   |   |     ||||||||| |||||  | || |||||| ||||||| || || || || ||||||||||||||  |||| || || ||||||||||||||||| || |||||| 
gtaacgaactcgcatccgatttccccaatactttcttcgattctttcctgttcctcaccttggttcgatctgccacgccggtgcagATCCGGTTCATCCTGCTGCAGAACCGGCAGGGGAAAACACGGCTGGCCAAGTACTATGTCGCTCTCGAGGACTCCGAGAAGCACAAGGTTGAGTACGAGG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 1
----------------------------gtactctct-cgattatgatgattcaatcttgattgcgaggagattgagttgct------gactcgttcat-taatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG-
                             | | |||    ||||  || ||    ||||  || | |      |   || |        | |||||    |  | |  |  || |||||||||||||||  |  | ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||||||||||||||||||||||||||| 
gttccttcgttcatcattctattccctctttcgctccataattacaataataatctcttcgttccaatatttcttttttccattctaaaattcgttttcctcttttccgcattcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGACTCCGAGAAGCACAAGGTCGAATACGAGG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 1
gtactctctcgattatgatgattcaatc--ttgattgcgaggagattgagttgctgact-cgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
|| |  ||   ||| |  |   ||  ||  |  |||          |   |   ||| |   |||     | |  |  || |||||||||||||||  |  | ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||||||||||||||||| |||||||||
gttcgttcataattctattccctctttcgttccattttttttttcatttttgaatgattgttttcccctttttccgcattcgcagATCCGATTCATTCTGTTGCAGAACAGGCAGGGCAAGACCCGTCTTGCCAAATACTACGTTCCTCTCGAGGATTCCGAGAAGCACAAGGTGGAATACGAG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 1
--gtactctctcgattatgat--gattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttgg--cagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
    |||   |   || |  |    ||   | |   |||        |   | |     ||  | ||    |||   | || |  ||||||||||||||| |  | |||||||| || || ||||| || || ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||||
gtacactgctttatttctcttccactttgttttcctttgttcatgtctgacgctcaattctgatccacctctctcccaatttgtccagATCCGATTCATATTATTGCAGAACAGACAAGGTAAGACTCGTCTAGCCAAATACTATGTCCCTCTCGAAGAATCCGAGAAACACAAAGTCGAATACGAG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 1
gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatct-ttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
                  ||| |  || ||   |  ||   |       ||||||  | |  ||     | |||  |  ||||||  |||||||  |  | || ||  | ||||| ||||| || ||||||||||||||||| || || ||||| ||||||||||| ||| || | || |||
-----------------gtgagtggattttcgcttggatccg-------tgctgagacatcgatcgccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 1
gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatct-ttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
                  ||| |  || ||   |  ||   |       ||| ||  | |  ||     | |||  |  ||||||  |||||||  |  | || ||  | ||||| ||||| || ||||||||||||||||| || || ||||| ||||||||||| ||| || | || |||
-----------------gtgagtggattttcgcttggatccg-------tgccgagacatcgatcgccgtgttggatgcgcagATTAGATTCATCCTCTTGCAAAATCGCCAGGGGAAGACTCGTCTCGCCAAGTACTATGTCCCGCTCGAAGACTCCGAGAAGCAAAAGCTCCAGTATGAG

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|37188193|gb|CF607542.1|CF607542
EST:     AGGTTCACCGTTTGTTCTGTGTGCCTCTGCAGCCAAGTCTTTGGAGAATG                         ATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAG
genomic: AGGTTCACCGTTTGTTCTGTGTGCCTCTGCAGCCAAGTCTTTGGAGAATGgtactctctc ... gatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAG
EST: gi|71886235|gb|DT035290.1|DT035290
EST:     AGGTTCACCGTTTGTTCTGTGTGCCTCTGCAGCCAAGTCTTTGGAGAATG                         ATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAG
genomic: AGGTTCACCGTTTGTTCTGTGTGCCTCTGCAGCCAAGTCTTTGGAGAATGgtactctctc ... gatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgattgcgaggagattgagttgctgactcgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG
                                   attaatctttgattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctctcgattatgatgattcaatcttgattgcgaggagattgagttgctgactcgttcattaatctttgatttggcagATCCGATTCATAATTCTACAGAACAGGCAGGGCAAGACCCGCCTCGCCAAGTACTATGTTCCTCTTGAAGAATCCGAGAAGCACAAGGTCGAATACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC