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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctacaacttttgttaccagtttgtgtctatttgctttcttgtgtaatcaattctgtggttgcataatgttaatgttttcttattttattttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTTCCTGTTTCTTCCCTGGCAGAGCCCATGAATGTTGAAAATCAG

Basic information

species Vitis vinifera
transcript Vv04s0044g01840.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G09370.2 (Glycine max), 3'ss of exon 5
----tagctacaacttttgttaccagtttgtgtctatttgctttcttgtgtaatcaattctgtggttgcataatgttaatgttttcttattttattttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTTCCTGTTTCTTCCCTGGCAGAGCCCATGAATGTTGAAAATCAG
     |  |  | |   | ||     |||    ||||    ||| || |  |      |      || | | ||  |     ||| | || |    | |  ||||||||||| ||||||||||| ||||||| ||  || |||||||| | ||| |||||| |||| |   ||||||| || ||| |||||||||||
cagaaaattgtatcagatattgtgcctttagtactatgcagtttgttatcca--tgtcttaacccttacttcattcttgctgtttgtgatatc--ctacaccagGCACTTCTTGATTATGAAAGACATAAAATACAAGGTGGTGAGCTGAATGTGCCTGTTGCTTCTCATCCAGAGCCTATAAATATTGAAAATCAG

upper sequence: Vv04s0044g01840.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G36040.1 (Glycine max), 3'ss of exon 5
--tagctacaacttttgttaccagtttgtgtctatttgctttcttgtgtaatcaattctgtggttgcataatgttaatgttttcttattttattttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTTCCTGTTTCTTCCCTGGCAGAGCCCATGAATGTTGAAAATCAG
   |  || | |   | ||     |||    ||||    ||| || |  | |    |      |||| | ||  |     | | | || |    | |  ||||||||||| ||||||||||| ||||||| |   || |||||||| | |||||||||| |||| |   ||||||| || ||| |||||||||||
gtaaattatatcagatattgtgcctttagtactatgcagtttgttatccatttctattaacccttgcctcattcttgctgtctgtgatatc--ctacaccagGCACTTCTTGATTATGAAAGACATAAAATAAAAGGTGGTGAGCTGAATGTTCCTGTTGCTTCTCATCCAGAGCCTATAAATATTGAAAATCAG
















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|110703600|gb|EE080590.1|EE080590
EST:     GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG                         GCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
EST: gi|32248497|gb|CD714316.1|CD714316
EST:     GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG                         GCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
EST: gi|32249759|gb|CD715578.1|CD715578
EST:     GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG                         GCACTTCTGGATTATGANAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
EST: gi|32247711|gb|CD713530.1|CD713530
EST:     GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG                         GCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
EST: gi|110688872|gb|EE067920.1|EE067920
EST:     GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAG                         GCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GACATGTACTACTGTTTCATGGACATTTCGAGGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
EST: gi|71880737|gb|DT029792.1|DT029792
EST:     GGTTTTTATGAGAAG                         GCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT
genomic: GGTTTTTATGAGAAGgtgatcatta ... ttttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcaattctgtggttgcataatgttaatgttttcttattttattttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTTCCTGTTTCTTCCCTGGCAGAGCCCATGAATGTTGAAAATCAG
                        tgttaat  putative branch site (score: 3)
                              tgttttcttattttat  CT-rich tract
                    ataatgttaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctacaacttttgttaccagtttgtgtctatttgctttcttgtgtaatcaattctgtggttgcataatgttaatgttttcttattttattttcttcagGCACTTCTGGATTATGAAAGGCATAAAACACGTGGCGGTGAGCTCAGTGTTCCTGTTTCTTCCCTGGCAGAGCCCATGAATGTTGAAAATCAG

- -ctacaac
- - - - - - -tgttacc
- - - - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg