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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgctaagcattaatctcacatgcaaactccagattggactaacggaatatttttttagagaggatgtaaactggctgtatattgatatgttcttttagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTTGATCTACACTTAACTCCGTACAGAGTACTAGCAACTGGACAGGATGAAG

Basic information

species Vitis vinifera
transcript Vv01s0127g00430.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA04G10090.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------gtaaatgctaagcattaatc-tcacatgcaaactccagattggactaacggaat----atttttttagagaggatgtaaactggctgtatattgatatgttcttt---tagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTTGATCTACACTTAACTCCGTACAGAGTACTAGCAACTGGACAGGATGAAG
                                                                ||  ||   | |||  ||    ||| |||     |  |     ||  ||| | |    ||   | |  ||| || || |  ||  | || ||  || |   ||||   |||||||||||||||||||| || ||||||||||||||||| ||||| ||||||||||| ||| |||| || ||||  || |||||||||||||| |||||||
gtattcctaccaatccttcttctgtcaccctgttatgcatgcaaatgaatacctgtgtacatgtgtggat-tgatgcaccaaaaaccacgtgcctgtccatgtgctcacacacgcactcatgatggatatttagaagacgtgagttgaat-tacataaatgttggctttatgtagGTTGTTCAAATGGTATCACTAATGGATCGATTGCTTAAGTTGGAAAATCTTGATCTGCACCTAACACCATACAAGGTGCTAGCAACTGGACAAGATGAAG

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA06G10090.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------gtaaatgctaagcattaat---ctcacatgcaaactccagat--tggactaacgga-atatttttttag---------agaggatgtaaact-ggctgtatat-tgatatgttcttttagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTTGATCTACACTTAACTCCGTACAGAGTACTAGCAACTGGACAGGATGAAG
                                                      ||| |   |  ||||| ||   |  | |  || |  || |    ||  || ||  | | |   |  |           ||| ||  | |  |    |  |||  || |    |  | |||||||||||||||||||| || ||||||||||||||||| || || ||||||||||||||| |||| || ||||  || |||||||||||||| |||||||
gtattccaaccaatccttcttctgtcaccctgttatgcatgcaaatgaatacctgtacaca-tgtgcattgatgcaccgaaaaacacatgcctgtccatgtgctcacacacacacactcctgatggatatttagaagacatgagttcaattacataaatgttggtcttatgtagGTTGTTCAAATGGTATCACTAATGGATCGATTGCTTAAGTTAGAAAATCTTGATCTACACCTAACACCATACAAGGTGCTAGCAACTGGACAAGATGAAG
















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|27584745|gb|CB007440.1|CB007440
EST:     GTTGCAAGATCATATTTAAGAAGGGGGATGATATTCGACAAGACCAATTG                         GTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTT
genomic: GTTGCAAGATCATATTTAAGAAGGGGGATGATATTCGACAAGACCAATTGgtaaatgcta ... gttcttttagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatatttttttagagaggatgtaaactggctgtatattgatatgttcttttagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTTGATCTACACTTAACTCCGTACAGAGTACTAGCAACTGGACAGGATGAAG
                                    tattgat  putative branch site (score: 3)
                                            tgttctttt  CT-rich tract
                                  tatattgatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgctaagcattaatctcacatgcaaactccagattggactaacggaatatttttttagagaggatgtaaactggctgtatattgatatgttcttttagGTTGTTCAAATGGTATCTCTCATGGATCGATTGCTTAAATTGGAGAATCTTGATCTACACTTAACTCCGTACAGAGTACTAGCAACTGGACAGGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG