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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacatatttggtctcctatccctctcttactgtttttctattcattggtcctatttattgaaatactttaggatttccttttctcaattctggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTTCTATTGTCGAAGGCAGGAAGATATGCTCAGCTGTGGGGCCAGCAAAATA

Basic information

species Vitis vinifera
transcript Vv06s0004g08350.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 18
aacatatttggtctcctatccctctcttactgtttttctattcattggtcctatttattga-aatactttaggatttccttttctcaatt--ctggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTTCTATTGTCGAAGGCAGGAAGATATGCTCAGCTGTGGGGCCAGCAAAATA
   | |     ||     |  |  |   | | | |||   ||  |  ||  | | | |||| ||||| |||             | | ||  |   | ||||||| |||||| |||| || |||| ||||||||| || ||||| |||||||| || ||||| || |||||||||||||| ||||||||||| ||||||||||
---aaagaaaatccatccttacaataacagtatgttttacttggtatgtattctcttttgacaatacattatttacattaaagattattttgccaatgttcagATCATTGTTTTGGAAAATGGGAAGGTGATTGAGCAAGGACCCCATGAAGTGCTCTTGTCAAAAGCAGGAAGATATGCACAGCTGTGGGGACAGCAAAATA

upper sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA14G38800.1 (Glycine max), 3'ss of exon 18
--------aacatatttggtctcctatccctctcttactgtttttctattcattggtcctatttattgaaatactttaggatttccttttctcaattctggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTTCTATTGTCGAAGGCAGGAAGATATGCTCAGCTGTGGGGCCAGCAAAATA
        |  ||| ||    |  |||   |  |||  | |   | |  || || | |  ||  |||    ||| |||  |  |  ||||| ||||       ||||||| |||||| |||| || |||| ||||||||| || ||||| |||||||| || || || || |||||||||||||| ||||||||||| ||||||||||
ccatccttacaatagttatcattttatgttttacttggtatgcatattctcttttgaca-atacattttt-tacattaaaagattgttttcccaatg------ttcagATCATTGTTTTGGAAAATGGGAAGGTGATTGAGCAAGGACCCCATGAAGTGCTCTTATCAAAAGCAGGAAGATATGCACAGCTGTGGGGACAGCAAAATA
















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|30256194|gb|CB972037.1|CB972037
EST:     CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAG                         ATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTT
genomic: CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAGgtaactatta ... tggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTT
EST: gi|30256126|gb|CB971969.1|CB971969
EST:     CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAG                         ATTATTGTTCTGGAGAACGGGACGGGGATTGAACAGGGACCACATGAAGTT
genomic: CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAGgtaactatta ... tggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTT
EST: gi|352778181|gb|FQ468843.1|FQ468843
EST:     CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAG                         ATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTT
genomic: CTTCAATCTTTATAGCACATAGACTTACAACTGCGATGCAGTGTGACGAGgtaactatta ... tggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcctatttattgaaatactttaggatttccttttctcaattctggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTTCTATTGTCGAAGGCAGGAAGATATGCTCAGCTGTGGGGCCAGCAAAATA
                            tttccttttctcaatt  CT-rich tract
      tatttattgaaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacatatttggtctcctatccctctcttactgtttttctattcattggtcctatttattgaaatactttaggatttccttttctcaattctggttttcagATTATTGTTCTGGAGAACGGGACGGTGATTGAACAGGGACCACATGAAGTTCTATTGTCGAAGGCAGGAAGATATGCTCAGCTGTGGGGCCAGCAAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - -tctccta
- - - - - - - - - -ccctctc
- - - - - - - - - - - - - - - - - - -ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac