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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG

Basic information

species Vitis vinifera
transcript Vv09s0002g02470.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 2
gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgt-tcttgtttc-tttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTA---GGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
             ||    ||  |  ||   |  | || ||    ||     | ||    | ||  | |||||| ||  |   ||      | || |||     ||||      ||| |||   |    ||||  ||   |||||   | || ||  |  |||   ||||||| |||||||| || |||||||||||||| ||||||||||| |||
------------gtatgtatatggaact---gactgtgcattttcacaaaggaagtcatatgaccttgtcttgtctcgctctgatgactgaacatattttctttctgtttcccttagAATGCCTGT---AGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAG

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 2
gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttgataggttgcctta-ctgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAA--GAAGGGATCTTGAGAGGATGGACTACCCAATT---AGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
                                           ||     | |   |  || |  | |    |||||||     | | |  | |  | ||| |    ||| | ||     |||   ||   | || || ||||||||    || ||||| |||   |||||||| ||||| ||||| || ||||| |||||||| ||||||||||||
-----------------------------------------gtaagtaccacacactatctaagttatgtaggtttcttgtttaaatctcttgttctcatagaagtcaatttata-tgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCATCCTGAATTCCGTTACAAGACTGAATTTCAGAGTCATGAACCTGAG

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 2
gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttg-ataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATT---AGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
                   ||    | || |  |  |  | | ||   || | |  ||  |   ||||  |    |   | || || ||  | | | | |   ||    |   |||||||   |    ||||  |||  |||||     ||  |  | ||    |||||||| |||||||| || |||||||||||||| ||||| ||||| |||
------------------gtatgcatattgaactg-tacaccaaagtctgcagactttttccctctgtattcagatggctaaacat-attttgtttgttttttcttcctt---tagCATGCTTGT---AGAAAAGATGCTGAGAAAGCTGATCATTCTATCAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCACGAACCAGAG

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 2
----gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATT---AGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
    |    || |||  | |  | | || | |||   |     |   ||||   ||||||| ||||  | | |         | |||||| | | || | | |   ||| ||  || ||||||| ||||||||||||||| | ||||||||||||||  | |||   |||||||| || || ||||| ||||| ||||||||||| ||||| || |||
gtaagactattttttgcttatgcaagtg-tttttgtgtaaaaaaaaaaaaccaaataggtt-ccttgttatgcac-------ttaatattgtaacatgtatgttttctgaaacatgcagCATGGTGGATCAAGAAGGGATTTGGAGAGGATGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCATGAGCCAGAG

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 4
gtgcgttcttttttaacactactggtctttagtttctgtatccaaacttg--ataggttgccttact---gttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
                               || | |  |    | ||||  || | ||  || |     | | | | |  |||   |  |||| | |  ||  |  ||||    |  ||    | ||| | ||||| || |||||       || || ||| | |||||||| || |||||||||||||| ||||||||||| ||||| ||||||
-------------------------------gtatgtccactttaccttgtaatcgtttttctgatatgggatttggatcattttggttatatgttgttgttgcatgctgtggattacagAGCAGTGGAACCAGAAGAGAGCTTGAAGAAGCTGATTATCCACTGAGGCATCCAGAGTTTCGTTATAAAACAGAGTTTCAGAGTCATGACCCTGAG

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------gtgcgttcttttttaacactac-tggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaat-------attat--gatatctttatacactgta-atgtgtagCATGGAGGATCAA-------GAAGGGATCTTGAGAGGATGGACTACCC---AATTAGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
                   ||||    ||  |||| | |   |||| | |   | |     |        |  |||||    ||| ||| || ||  |  | |       || |   || |  |||  |   |||   ||||  | |  ||| | |||       |||| ||  | ||||||  |||  | ||   |   ||||||||||||| |||||||   || |||||||| |||||||||||||||
gtaagactcatttctaaaagtgctactttcattaatattgtgtggtatatcagtccatccccgtcgtagaaccggttgttgaacttttcgtggtttctatagtcatctggatcactggaaactttttcatcttgtttgtgtgctggactgagcagCAACGAACTCGAAGAGAATTGGAGAGGGCGGATCATCCTGCACCCAGGCATCCCGAATATCGTTATGCGACGGAGTTTCAAAGCCATGAACCTGAG

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|71858308|gb|DT007363.1|DT007363
EST:     GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGAT                         CATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT
genomic: GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgttctt ... taatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT
EST: gi|161716360|gb|FC066871.1|FC066871
EST:     GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGAT                         CATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT
genomic: GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgttctt ... taatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT
EST: gi|161719206|gb|FC066075.1|FC066075
EST:     GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGAT                         CATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT
genomic: GTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgttctt ... taatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtagCATGGAGGATCAAGAAGGGATCTTGAGAGGATGGACTACCCAATTAGGCATCCCGAATTTCGTTATAAAACTGAGTTTCAGAGCCATGAACCTGAG
 gccttac  putative branch site (score: 3)
            tttctttcaatattat  TA-rich tract