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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctctctttctctcactaaagccctaaattccctttttttttttttgtgttttcatttgcgttcctgatattaaatttctcctctgatgttgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC

Basic information

species Vitis vinifera
transcript Vv18s0001g13180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 1
---------------------------------------gtgctctct-----ttctctcactaaagccctaaattccctttttttttttttg---tgttttcatttgcgttcctga--tattaaatttctcctctg-atgtt-gcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC
                                        | | |||         |||| |    ||||  | |  || |  ||| |||| |   | ||||  | |   |  ||||  | ||    |     | ||  |||| | | ||||| | ||||||||||| ||||| || || ||||| ||||| | ||| |||||||||||||||||  | || |||||||| || ||||| || ||||| |
gtaccaaaccctaaccctaaccccctcctctctaccctcatcccctccggatcccatctcccctccgccccgattcgccgtaatttgttttgggggtttttttctctctctctctgagctgtttgtgtgtgtgtatgtgtgttcgtgcagGTGCTGAGCAAGATCGCGTGCAACCGGCTGCAGAAGGAGCTCGCGGAGTGGCAGGTCAACCCTCCCTCCGGCTTCAAGCACAAGGTCACCGACAATCTCC

upper sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G116840_T01 (Zea mays), 3'ss of exon 1
----------------------------------gtgctctctttctctcactaaagccctaaattccctttttttttttttgtgttttcatttgcgttcctgatattaaatttctcctctgatgt-------tgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC
                                   | |  ||   |        | | |     |    ||   |  | ||  ||||| ||      |  |||   |    | ||  | |  |||         | | |||   | ||||||||||||||||  ||||| ||||| ||||| | ||| |||||||||||||| || ||||| |||||||| |  ||||| ||  | || |
gtaagaatctctagaccatctcccgaccgcccacatccgatccagccgcgtgcgaggtcgccgttcgatttgactgatcttgctgtttccacccctttgtctgggttcctttctccgcacacatgggtgcgcgcgtgcagGCTCTGAGCAAGATCGCCTGCAGCCGCCTGCAGAAGGAGCTCGCGGAGTGGCAGGTCAACCCGCCCGCGGGCTTCAAGCACAGGGTCACCGACGACCTCC

upper sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 1
----------------------------------gtgctctctttctctcactaaagccctaaattccctttttttttttttgtgttttcatttgcgttcctgatattaaatttctcctctgatgt-------tgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC
                                   | |  ||   |        | | |     |    ||   |  | ||  ||||| ||      |  |||   |    | ||  | |  |||         | | |||   | ||||||||||||||||  ||||| ||||| ||||| | ||| |||||||||||||| |                                    
gtaagaatctctagaccatctcccgaccgcccacatccgatccagccgcgtgcgaggtcgccgttcgatttgactgatcttgctgtttccacccctttgtctggGTTCCTTTCTCCGCACACATGGGTGCGCGCGTGCAGGCTCTGAGCAAGATCGCCTGCAGCCGCCTGCAGAAGGAGCTCGCGGAGTGGCAGGTCAACCCGC------------------------------------

upper sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgctctctttctctcactaaagccctaaattccctttttttttttttgtgttttcatttgcgttcctgatattaaatttctcctctg-atgt-tgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC
      ||| |||||||||   || ||        || |||   ||| || ||   ||| | |||  |||   ||  ||      |||  ||| |  ||||    | || ||||||||    ||||| || ||||||||||| |||||||||||| | || || ||| | || ||||| || |||||||| |||||||| |
----gttctctctctcactt--gctctg------tttatttaactttggttttggaattagggtttttgactatattttgggaaactgtgtgtgtatgtagACTCTGAGTAAGATCGCGACTAATCGTCTTCAGAAAGAGCTTGTGGAATGGCAGATGAATCCACCTACTGGTTTCAAACACAAAGTCACTGATAATCTCC

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|32248401|gb|CD714220.1|CD714220
EST:     TCTCTCTCCTCGAAGAAACAATGACCAGTTCATCTGCCCCTTCTCGCAAG                         GTGTTAAGCAAGATCGCCTGCAATCGTCTCCAGAAAGAGCTGGTGGAATGG
genomic: TCTCTCTCCTCGAAGAAACAATGACTAGTTCATCTGCCCCTTCTCGCAAGgtgctctctt ... tgttgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGG
EST: gi|71874807|gb|DT023862.1|DT023862
EST:     TCTCTCTCCTCGAAGCAACAATGACCAGTTCATCTGCCCCTTCTCGCAAG                         GTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGG
genomic: TCTCTCTCCTCGAAGAAACAATGACTAGTTCATCTGCCCCTTCTCGCAAGgtgctctctt ... tgttgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGG
EST: gi|32267803|gb|CD716962.1|CD716962
EST:     TCTCTCTCCTCGAAGAAACAATGACCAGTTCATCTGCCCCTTCTCGCAAG                         GTGTTAAGCAAGATCGCCTGCAATCGTCTCCAGAAAGAGCTGGTGGAATGG
genomic: TCTCTCTCCTCGAAGAAACAATGACTAGTTCATCTGCCCCTTCTCGCAAGgtgctctctt ... tgttgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgttttcatttgcgttcctgatattaaatttctcctctgatgttgcgtagGTGTTAAGCAAGATCGCCTGCAATCGCCTCCAGAAAGAGCTGGTGGAATGGCAGGTCAACCCTCCTGCGGGATTCAAGCATAAAGTCACAGATAATCTAC
                       tgatattaaatttct  TA-rich tract