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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagctaacgctataagctttcatgtattaactgctgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG

Basic information

species Vitis vinifera
transcript Vv02s0025g00240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g03370.2 (Oryza sativa), 3'ss of exon 2
gtaagttagctaacgctataagctttcatgtattaactgctgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
    || |||  || | | | ||   | |         || |       || |   ||   || ||  | |    |   |||  ||      ||||||||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
----gtaagcgcacac-acacgcac-cgtccgcacgacgccgcgcgtcgctcgtgtaaccgtgttgg-ttttgcct---tgccattttgcg-cagGTGGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTGTGGCACGCGTCGCTGTGGCACATGCACGAGTCGCACCACCGCCCGCGAGACGGGCCGT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g38940.1 (Oryza sativa), 3'ss of exon 1
---------------------------------gtaagttagctaacgctataagctttcatgta--ttaactgctgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatca----gGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG
                                  |||| |  |   |||  |     ||  || |      | || |  |  | |  |  ||  || ||||     || ||  | | ||| | |         ||||||||||||||| |||||||||||||| |||                                       
gttcgtactctcggcctagctcgccgccgtcatctaaggtgacacgcgcattgtttcttggtgcagGCCGGCGGCGGCGACGTTCC-GGCGACGGA-GATGGTCGGCACGTTCGCGTTGTCGGTGGGGGCGGCGGTGGGGATGGAGTTCTGGGCGCGGTGGGCGCACC--------------------------------------

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G382534_T01 (Zea mays), 3'ss of exon 2
-------------------------gtaagttagctaacgctataagct---ttcatgtattaactgctgaaa-aatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
                          |      |    |||  |  | |   |||||| ||  |  | || |   |||  ||  |     ||| |  |     |||||||  |||      ||||||||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
gtgagttcgcccactcgtcctcggcatgccgcgggccgcgccgtgtggtgggttcatggatggatggatggatcgatctgtggcgcggactgacgtgtt---ggtgggtg--gtttgcgtgcagGTGGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTGTGGCACGCGTCGCTGTGGCACATGCACGAGTCGCACCACCGGGCCCGCGACGACGGGC

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G090051_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------gtaagttagctaacgctataa---gctttcatgtattaactgct-gaaaaatccttgaagaaagatgatgaatctcaagtgggtgctg--ttg-attatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
                                            | | |         | | |     ||||||   | |   | ||  ||  |||   |     | ||  |  |||| |  || |||| ||  ||| |||  ||||||||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||| ||                            
gtgagttccagagttcccagactcgtcctcctcgcagccacgcggcacgccccgccgtggtctggggcgctttctcttctgcgccgcgagacgaatggataccagacgaccaacaatcgcgtgttggtggtggtttgcatttgcagGTGGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTGTGGCACGCGTCGCTGTGGCACATGCACCAGTCCCACCACCGGCCCCGCGACGGGCCCT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
gtaagttagctaacgctataagctttcatgtatt---aactgctgaaaaatccttgaag-aaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
||| |   ||   |  |   ||||    | |||    ||||  |      | | ||| |  ||  ||      ||    |||| || ||   |   ||||| ||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
gtacgc-ggcggtccttggcagctcagctctatctccaactttttttcctttcctgacgcgaaactgggctgacttccctgggcgc-gtccgtg--cagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G152135_T06 (Zea mays), 3'ss of exon 2
gtaagttagctaacgctataagctttcatgtattaactgctgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
||| |        | | |    ||||  ||       |||    | |||   ||     |       || ||  |  |||   ||   |   ||||| ||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
gtacgcggcgctcctcgacgtccttttctgacgcgcatgcaagcagatc---gattggggcctgctgatttc--gctggtcgcgtgcgtg--cagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTGTGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGCCGCGCGAGGGCCCCT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G164318_T01 (Zea mays), 3'ss of exon 2
-----------------gtaagttagctaacgctataagctttcatgtattaactgctgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattat-----cagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
                     |  ||||   |||  || ||||  |        | |   |        |   ||    | ||| |  |  | | | |    ||  | |     ||||| ||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
gtacgcggcgctgcgctcctcggcagctctagctccaacctttttttcccccctttcctgacgcgaaaggcgaaactgggctgatttccctgggcgcgtccgtgcgtgtgcgtgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTGTGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGCCGCGCGAGGGCCCAT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G163683_T02 (Zea mays), 3'ss of exon 2
gtaagttagctaacgctataagctttcatgtattaactgctgaaaaatccttgaagaaaga-tgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG----------------------------
                  | |||| | || |   ||||  |      | | ||| |  | | ||      ||    |||| || ||   |   ||||| ||||||||||| |||||||||||||| |||   ||||| ||||| || || |||||||| |||||||||                            
----------------gctcagctct-atct-ccaactttttttcctttcctgacgcgaaactgggctgacttccctgggcgc-gtccgtg--cagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT

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|26258277|gb|CA809340.1|CA809340
EST:     TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCT                         GTGGGGATGGAGTTTTGGGCTCGGTGGGCTCACAAAGCGCTCTGGCATGCT
genomic: TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCTgtaagttagc ... tgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCT
EST: gi|26257470|gb|CA808533.1|CA808533
EST:     TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCT                         GTGGGGATGGAGTTTTGGGCTCGGTGGGCTCACAAAGCGCTCTGGCATGCT
genomic: TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCTgtaagttagc ... tgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCT
EST: gi|294964011|gb|GW836886.1|GW836886
EST:     TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCT                         GTGGGGATGGAGTTTTGGGCTCGGTGGGCTCACAAAGCGCTCTGGCATG
genomic: TCCCAGTTCTGGAAATGTTGGGTACATTTGCTCTTTCTGTGGGAGCTGCTgtaagttagc ... tgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaatccttgaagaaagatgatgaatctcaagtgggtgctgttgattatcagGTGGGGATGGAGTTTTGGGCGCGGTGGGCTCACAAAGCGCTCTGGCATGCTTCACTGTGGCATATGCACGAG
                                          tgttgat  putative branch site (score: 4)
                                            ttgattat  TA-rich tract