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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT

Basic information

species Vitis vinifera
transcript Vv14s0060g01750.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g24750.1 (Oryza sativa), 3'ss of exon 2
tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
                          || | |||  |   |   | | | ||  |          | || | |  | |||      | |      |  |||| || |||||||| || || ||||||||  || |  ||||||| ||||| |||||||| ||||||||| |||| || ||||||||||| |||||||| |
-------------------------gtaagcactaattattttgatctttattttgtctgttga-gatctatataacaatttcagcatgaatgtctttagGTTGTTGAGGATGGCTACGAGTTCTTTGCGCAAAGGAGATTAGTGACAATCTTTTCAGCTCCAAACTATTGTGGGGAATTTGATAATGCGGGTGCTCTGT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
--tcataccag-ccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
  |  |   || | | |||   || | | |    | |  | | || |    | ||  | |   |      | | | |      || |  | |         ||||||| || ||||| ||||| ||||||||  ||||| ||||||| ||||| |||||||| ||||| ||| ||||||||||||||||||  || |||||||
gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttac--ctgacaatgctggca-----cgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G137286_T02 (Zea mays), 3'ss of exon 2
--tcataccag-ccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
  |  |   || | | |||   || ||| |    | |  | | | | |   | ||  | |   |      | | | |      || |  | |         |||| || || ||||| ||||| || |||||  ||||| ||||||| ||||| |||||||| ||||| ||  |||||||||| ||||| ||||||||||| |
gtttgtgaaagtctatcttctatcctattttatcaattatcttttacattttgatctttac--ctgacaatgctggca-----cgcttcatgaatggccctagGTAGTTGAAGATGGTTATGAGTTTTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTACTGTGGAGAGTTCGATAACGCCGGTGCTCTGT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 2
--tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
   | | |   |   ||| |  | |        |   ||  ||  |  || | | ||   | ||||  | |     | |  |   | |    |   |   |||| ||||||||||||||||| || ||||||||| || |||||||||| || ||||| || ||||| |||||||| || ||||| ||||| |||||  | |
ttccttgctttcttactttaacctttgtcttttatgtgttacttcttccaacttcctctgatcaag--gcctcattttactttcctattttttttttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTATGGTGGGGAATTTGACAATGCTGGTGCGTTGT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G39440.1 (Glycine max), 3'ss of exon 2
-tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaat---cgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
 || | || ||    ||   | |    | |    |  ||| | |     | || | ||   |   ||||| ||     | |   | |||  |  |   |   |||| ||||||||||||||||| || ||||||||| || |||||||||| || ||||| || ||||| || ||||| || ||||| ||||| |||||  | |
atcttccctgcttttttactttaacctttgtcttttatgtgttac----ttattccaacttcctctggtcaaggtctcattttactttcctattttcttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTACGGTGGGGAATTTGACAATGCTGGTGCATTGT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatacta--aaaacaagtggtccagac-taaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
                                                   |   |        | |  ||  ||||| | || |   | |  | |  |  | |||   |  | ||     | |||  |  | | ||      |    |||||||| ||||| ||||| ||||| || || || |||||  | ||||||||||| || ||||| ||||||||||| ||||||||||| |||||||||||  | |
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaac-----aagtggt--ccagactaaaatcgttctaag---ctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
                       | ||| |  |  |||      ||     || | | || ||    ||| |  ||| | ||      | |  |  ||| |    |   ||   | |    ||   ||||||| || || || || ||||| || || || |||||  |||||||||| || || ||||| |||||||||||||| |||||||| || || |||||  | |
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgattagcgtttgtc--cataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT

upper sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 3'ss of exon 3
--tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
  |  ||| |          || || ||      ||  ||  |   |  | | || |        ||       ||| | || ||   ||  | |  ||||||| ||||||||||| ||||| || ||||||||||| |   | ||||| ||||| || |||||||| ||  |||| || ||||||||||| |||||  |  
gattttacaaattgtacaatgtgat-tcagtctcctaatgggtagaattaccttattcctggtgtgtttcaagtactgacat-gtgtgaatgtcacatgcagGTAGTGGAGGATGGTTATGAGTTTTTTGCTAAACGCCAGCTGGTCACTATTTTCTCTGCACCAAATTACTGTGGTGAATTTGATAATGCGGGTGCGATGA

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|27581472|gb|CB004167.1|CB004167
EST:     CTGAATTTTTGGACAAGAATGATCTTGATCTCATTTGCCGAGGTCATCAG                         GTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
genomic: CTGAATTTTTGGACAAGAATGATCTTGATCTCATTTGCCGAGGTCATCAGgtaagcaaag ... tgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
EST: gi|110393373|gb|EC958562.1|EC958562
EST:     AAGAATGATCTTGATCTCATTTGCCGAGGTCATCAG                         GTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
genomic: AAGAATGATCTTGATCTCATTTGCCGAGGTCATCAGgtaagcaaag ... tgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
EST: gi|110429218|gb|EC995708.1|EC995708
EST:     CTGAATTTTTGGACAAGAATGATCTTGATCTCATTTGCCGAGGTCATCAG                         GTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
genomic: CTGAATTTTTGGACAAGAATGATCTTGATCTCATTTGCCGAGGTCATCAGgtaagcaaag ... tgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT
EST: gi|30328639|gb|CD011901.1|CD011901
EST:     TTTGCCGAGGTCATCAG                         GTGGTGGAGGATGGATATGAATTCTTTGTTAAACGACGATTAGTCACAATT
genomic: TTTGCCGAGGTCATCAGgtaagcaaag ... tgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT
     atactaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataccagccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - -ccagcca
- - - - - - - - - - - - - - -ggactgg
- - - - - - - - - - - - - - - - - - tgtctga
- - - - - - - - - - - - - - - - - - - - - - - - - - actaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa