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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaaccatgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat...

Basic information

species Vitis vinifera
transcript Vv07s0141g00290.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0141g00290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 3
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttc---ttccaaccatgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat---------------------
    || |||    ||| ||    ||||||| | ||||  |||| |||| || |||||||| ||||| || |||||||| |||||||||||||| ||| |||| |||     | ||  | || |            |   |   | | |  |  | | |   | ||   | ||| |  |||   |    || |   |  || |                     
---GGAACAAT---ATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAGACAAGGATGGTGACTGGATGCTTGTTGGAGATGTCCCGTGGCAgtatgttactacttcattcttgtgcccccttaactgttttccttattttccacctcatgattagaatgcggtttagcgataccacgttcaagtttctcgcattagctgattggttactctgcag

upper sequence: Vv07s0141g00290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G159285_T01 (Zea mays), 5'ss of exon 3
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaacca-tgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataat-tctaaaaaatgattatcaat----
||||| | ||  |  | ||||   | |  |||  ||||   ||  | || ||||||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||| |   | | || |   |    ||        |  |   | || ||  |         || || | | ||  |  ||     ||  || ||  |    
ATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATGTGGTCACTACTTACGAAGACAAGGATGGCGACTGGATGCTCGTTGGCGACGTCCCGTGGGAgtatgttctgcattctagtgtgccatcatctaggat-ttgatcaggcaaatgttcag----gcttcagcttcttatatgctgccttgttgattgttgtccctgcag

upper sequence: Vv07s0141g00290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G31530.1 (Glycine max), 5'ss of exon 3
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaaccatgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat--------
||||||||||| |||  |||||||||||  | | |||| |||| ||||| || || ||||| ||||| || |||||||| || || ||||||||||||||||||||  |||        |  | |     ||||||              |||   |     |||| | |  | |  || | ||| | ||| ||| |||         
ATGAGAGCAAGCTGAATGATCTTTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagtctttc--------acctctactcaaaatcaatttggccgcgataattgaactttgcaatattatggggataaactttaacatatgtttaccaaacttcacgt

upper sequence: Vv07s0141g00290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G34380.1 (Glycine max), 5'ss of exon 3
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaaccatgagtt---ttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat-
||||||||||| |||  ||||| |||||  | | |||| |||| ||||| || || ||||| ||||| || |||||||| || || |||||||||||||||||||| ||| ||||  |    |   |      ||||||        |     |||   |     ||||   |  |  |  | | ||| | ||| ||| |||  
ATGAGAGCAAGCTGAATGATCTCTTGAACAGCTCTGATTATGTCCCAACCTATGAGGACAAGGATGGTGACTGGATGCTTGTCGGTGATGTCCCATGGGAgtaagt-ctttcaactctactctacatcactcaaaatcaatttggccacgataattgaactttgcaata---tgggggaagactttaacacatgcttaacaaag

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|349828896|gb|FQ419229.1|FQ419229
EST:     CAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGA                         GATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC
genomic: CAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttctt ... ttccattcagGATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC
EST: gi|110690829|gb|EE068235.1|EE068235
EST:     TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGA                         GATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAAGGAAA-GAGG
genomic: TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttctt ... ttccattcagGATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAA-GGAAAAGAGG
EST: gi|110690342|gb|EE067357.1|EE067357
EST:     TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGA                         GATGTTTGTGGATTNCATGCAA-CGCTTGCGCATAATGAAAGGAAAAAGAG
genomic: TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttctt ... ttccattcagGATGTTTGTGGATT-CATGCAAACGCTTGCGCATAATGAAAGGAAAA-GAG
EST: gi|110374116|gb|EC938663.1|EC938663
EST:     TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGA                         GATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC
genomic: TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttctt ... ttccattcagGATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC
EST: gi|22011282|gb|BQ796316.1|BQ796316
EST:     TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGA                         GATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC
genomic: TACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttctt ... ttccattcagGATGTTTGTGGATTCATGCAAACGCTTGCGCATAATGAAAGGAAAAGAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGAGCAAGTTGATGGATCTTTTGAATGGTTTTGATCATGTTCCAACATACGAAGACAAAGATGGGGATTGGATGCTCGTTGGAGATGTCCCATGGGAgtaagttcttccaaccatgagttttggcttaaatcaccaaaaatatatatattaggcagaaaaatagtttttgaaataattctaaaaaatgattatcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat