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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

Basic information

species Vitis vinifera
transcript Vv05s0049g01230.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 3'ss of exon 2
tgtgtgtagtattttttatttttgaaatactt--tgaattgtgtcaa-gcacttatccatgtttact-tgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
| | |  ||| ||   ||| ||  |  |  |   |||| | ||  ||    ||| |  || || ||  ||   ||||||       ||||||     |  | |||| || || ||||| || || || || || ||||||||||| ||||| |||||||| || || || ||||||||||||||| ||||
tttattcagt-ttaaatatgttgtaccttttcaatgaactttggtaatatccttttgtattttgaccatgatgttgatatgataaatcatcttc---tttaaagGCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
-----tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
      ||         | ||  | ||     | | || | | |    | |   |    ||| || | | | |||  |     |     || |   |||  | |||| || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||
ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagc--taggttttctgacattttcaat-gcaat--actgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
 ||         | ||  | ||     | | || | | |    | |   |    ||| || | | | |||  |     |     || |   |||  | |||| || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||
ggttcaactggatcttagtcttcagtgttcgttcagtagc--taggttttctgacattttcaat-gcaat--actgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 2
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtc---------atctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
       | | |   | |  |      || | |  | ||| |||  || | | | | |||| ||   | ||     ||| | |          || |   |||  | |||| || ||||| || || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||
-------actttggctcaactggatcttagtcttcactgt-tcattcaat-agctaggtttgctgacattttgaggacaatatttctaacacaatttaccattttaaagGCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaa--gcacttatccatgtttacttgtaattgataaacattgtcatctgtaa---ttgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
        ||| |||| | |||   ||| || |||  | ||| ||  | | |||   | | ||  |   | | | |    | |    | |||     ||  ||||||||||||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| ||||| || ||||| |||||
--------gtacttttcagtttctcaat-ctgtgacctatgtgaattggagttaattagggtt-ttcaaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G40200.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaa--gcacttatccatgtttacttgtaattgataaacattgtcatctgtaa---ttgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
                                                                                   |   | | ||| |||| | |||   ||| || |||  | ||| ||  | | |||   | | ||  |   | | | |    | |    | |||     ||  ||||||||||||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| ||||| || ||||| |||||
gtagagattctattcccaatttccttgaaacgctctttccctctttccgttcactcgctccgttatgaagttcaggctgcgattcaattttgtacttttcagtttctcaat-ctgtgacctatgtgaattggagttaattagggtt-ttcaaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------------tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaa--gcacttatccatgtttacttgtaattgataaacattgtcatctgtaa---ttgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
                                                                                              |    ||||||| | |||   ||| || |||  | ||| ||  | | |||   | | ||  |     | |||| | |     || ||| |   ||    |||| |||||||||||||| || || || ||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| |||||
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaat-ctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 3'ss of exon 1
-tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
   |  || | |||| ||  || | ||  |  |  |  ||      | |   ||     || | ||  |  |  |     |||   | | |  ||   ||||| |||||||||||||| || || || |||||||||||||| ||||| |||||||||||||| ||||||||||| |||| ||||||
aattaggtcg-atttgtttcttataaagcatatatagatgaaatcgggaacaatttgctttaaatttaacatcttttggtttgggtttttttcttttgcagGCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------------tgtgtgtag-tattttttatttttgaaatactttgaattgtgtcaagcacttatccatgttta-cttgtaattg-ataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
                                                                                 |  | |||| |    | |       |  | ||||   |  ||| |||      |   |    | |   || ||   ||| |    |  | |||  |||  ||||| |||||||||||||| || || || |||||||||||||| ||||| || |||||||| || |||||||| || ||||  |||||
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT

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|110416715|gb|EC982713.1|EC982713
EST:     CTCAATCTAAGATGCAG                         GCCAGTGATAGGTTTATTATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
genomic: CTCAATCTAAGATGCAGgtgagagttt ... aattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
EST: gi|110686941|gb|EE063919.1|EE063919
EST:     CTCCGTAACTCTCTCTCGGCGTTTGTTGATTTTCTCAATCTAAGATGCAG                         GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
genomic: CTCCGTAACTCTCTCTCGGCGTTTGTTGATTTTCTCAATCTAAGATGCAGgtgagagttt ... aattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
EST: gi|110687101|gb|EE064219.1|EE064219
EST:     CTCCGTAACTCTCTCTCGGCGTTTGTTGATTTTCTCAATCTAAGATGCAG                         GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
genomic: CTCCGTAACTCTCTCTCGGCGTTTGTTGATTTTCTCAATCTAAGATGCAGgtgagagttt ... aattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
EST: gi|110731061|gb|EE108849.1|EE108849
EST:     TTGTTGA-TTTCTCAATCTAAGATGCAG                         GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA
genomic: TTGTTGATTTTCTCAATCTAAGATGCAGgtgagagttt ... aattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT
                      aattgat  putative branch site (score: 4)
                     taattgataaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaagcacttatccatgtttacttgtaattgataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
tgtgtgt
- - - - - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - - - - -tcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaac