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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

Basic information

species Vitis vinifera
transcript Vv09s0002g03640.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
    ||   ||||| |   |   |  |   |||| |  | ||  |       || ||    |  | | || | |       ||| |||||| |  |||||||  |||||||| ||||||||||||||||| ||| |||||||| | ||||||||||| || ||||| || ||  | || ||||||||| | ||  | |  |
----gtgagttttcttggatcaaaccgtttctttga-acttttta------ttcttcttggaagatcaaagtaatggtgttattcatgtttta--tttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
|| ||||   |||| ||| |  | |    ||  | || | || |        | |   | ||     ||  |      | |  || | ||    |||||||| |||||| |  ||||||||||||||||| |||||||||||| | ||||||||||| || ||||| |||||  | ||||| |||||| || | ||| | |
gttagttg--tttcttcaatcacct--ttaccgtgatccttttctgtaggattaaa--aataatgcttatgttgttttttctctattctt----atttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 21
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
|| ||||  || |    |    |||  |  |  || |   |||| |||      ||  | || |     |||||    |    |     ||    ||||||| ||||||    ||||||||||||||||| |||||||||||| | ||||||||||| || ||||| |||||  | ||||| |||||| |||| |||   |
gtcagtt-gttgtttcaatcaccatccctgcgatcct--tttcctacctgtaggattaaatagagg---actcatgttttttct--ctattcctgtttcagAGAATTCCTGGATGGTGGATCTGGTACTACTGGATTTGCCCACTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGGAAGACCTCA

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA15G02220.1 (Glycine max), 3'ss of exon 22
gtaagt-tcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
||||||  |||| |  |  |     ||  ||     ||       |  |    ||||   ||  ||  ||| |    | |  || ||  |||    |||||||||||||| || |||||| | ||||| |||||||||||||||||||||||||| || || ||| | || || || |||||||||||  | |||      |
gtaagtaccattctagtttggttattatgcatcaatataagaattactcg---tcatgttctctaacgtaatt---gcttgtatcaac-tttggcttttcagAAAATTCCTAAATGGTGGGTTTGGTATTATTGGATTTGCCCAGTAGCATGGACTGTATATGGGTTAATTGTCTCACAATATGGAGATGTAGAGATAGAGA

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA13G43140.1 (Glycine max), 3'ss of exon 21
gtaagttcattttcctcagtggcatagccactttcatgccttcc-aaccaacctcatccactacaaactaactcaaa-cctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
      | | ||     |  |  |||||   |||           ||  |  ||  ||   | |   |||||  ||  |||| || ||  ||| | ||||||||||||||| || |||||| | ||||| |||||||||||||||||||| ||||| || || ||| | || || || |||||||||||  | |||      |
aatgactaaattgataaaaagaaatagcttatttagcaataaaagaattattcttgtcattttct--ctaacataattcctctatcaac-tttgacatttcagAAAATTCCTAAATGGTGGGTTTGGTATTATTGGATTTGCCCAGTAGCGTGGACTGTGTATGGGTTAATTGTCTCACAATATGGAGATGTAGAGATAGAGA

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
|| ||| |  || |   |||  | ||     ||| ||     | | |  | || |   | | |  |||||   |  | || |  ||  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||||| ||||||||||| || ||  | || || || |||||| ||||  | |||||| || 
gtgagtaccattcc---agtttcgtaa----ttttattgaaacaagcatatcttacataatccttactaaaa-actcttctaccaac-tttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC

upper sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA-
|| ||| |  ||     | |  | |    |  || |  |     |||  | || |   | |    ||||||  ||  || |    |  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||||| ||||||||||| || ||  | || || || |||||| ||||  | |||||| ||  
gtgagtaccattct---aatttcgttattatattgaaaca----aacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGAC-CATC

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|161717628|gb|FC066907.1|FC066907
EST:     CTTTCTATGCAGTCTTCAATCTTTTCTCAGGCTTCTTCATCCCCAGACCA                         AAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCACTAGCATGG
genomic: CTTTCTATGCAGTATTCAATCTTTTCTCAGGCTTCTTCATCCCCAGACCAgtaagttcat ... aaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGG
EST: gi|294967137|gb|GW840012.1|GW840012
EST:     CGTTCTATGCAGTCTTCAATCTTTTCTCAGGCTTCTTCATCCCCAGACCA                         AAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGG
genomic: CTTTCTATGCAGTATTCAATCTTTTCTCAGGCTTCTTCATCCCCAGACCAgtaagttcat ... aaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA
                                   attaatgtttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA