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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtctccatcgttgaggaagaaatcactttatgggatgtctccaaagggcctcatgaagatgctactgaataacttgtataccagtctttttgcgtgtgctttccccctagaaatactggttttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC

Basic information

species Vitis vinifera
transcript Vv06s0004g07920.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G38390.1 (Glycine max), 3'ss of exon 2
gtatagtctccatcgttgaggaagaaatcactttatgggatgtctccaaagggcctcatgaagatgctactgaataacttgtataccagtctttttgcgtgtgctttccccctagaaatactggttttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC
                                                   |  ||||    | |   | | | |   ||| | ||     |  || |  || ||      ||   | || |  | || | | ||   |||||  |  ||| |         |||| || || ||||||||||||||||| || ||||||||| | ||||||||||| | |||||| |||||||||||||||||||| || |||||||| |||||
---------------------------------------------------gtactcactttggtttcaataagtg--ttgcacact----taattacaagtactaagaaactgctactatttttattgtcaattaaatttttcctcttttatgc-------tagGCACCCCTGAGTTCATGGCACCAGAATTGTATGAGGAAGAATACAATGAACTTGCTGATGTATACTCATTTGGCATGTGTGTTTTGGAAATGCTCACATC

upper sequence: Vv06s0004g07920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G40200.1 (Glycine max), 3'ss of exon 3
gtatagtctccatcgttgaggaagaaatcactttatgggatgtctccaaagggcctcatgaagatgctactgaataacttgtataccagtctttttgcgtgtgctttccccctagaaatactggt-tttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC
                                                   |  ||||  | ||| | | | | |   ||| | ||        ||||  || || | |    | || | ||  | ||| | | |      |   ||| | | ||   ||   |||| || || ||||||||||||||||| || ||||||||| | ||||||||||| | |||||| || |||||||||||||||||  | |||||||| |||||
---------------------------------------------------gtactcactatgattccaataagtg--ttgcacac--------ttgcaagtactgtactaaga-aactgctactatttattattgtcaaataaaattttctctttt-tgtgctagGCACTCCTGAGTTCATGGCACCAGAATTGTATGAGGAAGAATACAATGAACTTGCTGATGTATATTCATTTGGCATGTGTGTTCTGGAAATGCTCACATC

upper sequence: Vv06s0004g07920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G26210.1 (Glycine max), 3'ss of exon 4
gtatagtctccatcgttgaggaagaaatcactttatgggatgtctccaaagggcctcatgaagatgctactgaataacttgtataccagtctttttgcgtgtgctttccccctagaaatactggttttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC
                                                          | || |   || | ||    || | ||||| |   |||  |      ||  |  | || | | |      |||| |  ||| ||  |   ||| |    |    |||| || |  ||||||||||||||||| || ||| | ||| | |||||| |||| |||||||| ||||||||||||||||||||  | ||||||||||||||
----------------------------------------------------------tcaaaaacatatttaaatctttttctaccaatgaattt-tgcagatattgactattgagacaat------ctaattgttgtgttaaaaattttctccattatactagGCACCCAAGAGTTCATGGCACCAGAATTCTATAAAGAAGAATACAATCAACTTGTTGATGTGTACTCATTTGGCATGTGTGTTCTGGAAATGCTTACATC

upper sequence: Vv06s0004g07920.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G58350.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatagtctccatcgttgaggaagaaatcactttatgggatgtctccaaagggcctcatgaagatgctactgaataacttgtataccagtctttttgcgtgtgctttccccctagaaatactggttttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC
                                                                                ||||  |       | |  |||  |  |  | |     | |   |  | |  |||     | ||  ||||| ||   | | ||||| || || ||||||||||||||||| ||||||||||| ||||| ||||||||  |||| || || || ||||| |||||  | || || ||| | || ||
--------------------------------------------------------------------------------gtatgtctcaaaaatcgtttgttttcacttcttg----tccaaatcatatg-cttagacctctttgtgtttctt---ttgcatagGCACTCCTGAGTTCATGGCACCAGAATTATATGAGGAGAACTATAATGAACTCATTGACGTATATTCCTTTGGTATGTGCTTTTTGGAGATGATCACCTC

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|27579538|gb|CB002233.1|CB002233
EST:     AGGCTTGGCAGCCATTCTCCGGGGCTCCCAATCAGCCCACAGTGTTATAG                         GAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAAC
genomic: AGGCTTGGCAGCCATTCTCCGGGGCTCCCAATCAGCTCACAGTGTTATAGgtatagtctc ... ggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAAC
EST: gi|110711559|gb|EE088176.1|EE088176
EST:     AGGCTTGGCAGCCATTCTCCGGGGCTCCCAATCAGCCCACAGTGTTATAG                         GAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAAC
genomic: AGGCTTGGCAGCCATTCTCCGGGGCTCCCAATCAGCTCACAGTGTTATAGgtatagtctc ... ggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagaaatactggttttctaacttctgttttttattgtttgttgggtggtatagGAACACCGGAGTTCATGGCACCAGAGTTATATGAGGAAAACTACAATGAACTGGTTGATGTCTACTCATTTGGCATGTGTGTATTAGAAATGCTTACATC
                ttctaac  putative branch site (score: 1)
                            ttttttattgtttgtt  TA-rich tract