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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA

Basic information

species Vitis vinifera
transcript Vv17s0000g00620.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G17460.1 (Glycine max), 3'ss of exon 4
ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA
                  | |   | |  |||||  | |   |||| ||||       | |||  || |    || ||  || |||   ||||  | ||||||||||| || || || ||||||||||| || |||||||||||||||| |||||||| ||||||| | ||||||| |     |   || ||||||||||
---------------gtgagtaatcactttgtattaagtattaaccttgta-------tttgagatg-taacatatttcatatctttattctgtctgcagTTCTTTACCACAGAGCCCTATGCTTGTGAACCATCAAGTTTGCCAAAGTATCCTCCCAGCAAAGAATTGGATGTAAAACTGAGAGATGAGGAAGCAAGAA

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G37630.1 (Glycine max), 3'ss of exon 4
ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA
                |  | ||  ||| ||| ||       |||| ||||     | | | |  | ||    || ||  || ||    ||||  | ||||||||||| || || || ||||||||||| || |||||||||||||||| |||||||| ||||||| | ||||||| |     |   || ||||||||||
----------------gtgagtga-tcactgtgtatt-----aaccttgtatttgggatataatat-ataacatatttcatatctgtattctgtctgcagTTCTTTACCACAGAGCCTTATGCTTGTGAACCATCAAGTTTGCCAAAGTATCCTCCCAGCAAAGAATTGGATGTAAAACTGAGAGATGAAGAAGCAAGAA

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G38410.1 (Glycine max), 3'ss of exon 4
ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA
                         | | ||   || | || |   || ||| | |    |  |||   | || |||    || |  | |||   | ||||||||||| ||||| || ||||||||||| || || | ||| ||||||| |||||||||||||||| | ||| ||| |     |   || ||||||||||
------------------------gtgagtgatcac-tgtggattagtatagtatttgagtt-cttatgtattaactc---acgtattttctttctgcagTTCTTTACCACTGAGCCCTATGCTTGTGAACCATCTAATTTACCAAAGTATCCTCCCACCAAAGAATTGGATATAAAACTGAGAGATGAAGAAGCAAGAA

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G01250.1 (Glycine max), 3'ss of exon 4
ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgc-tctgacttgattgtttacttggtaccttgtct-ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAA---GCAAGAA
                              ||   |  |       |  ||| | ||  | |||  || |  | || |   |  ||||| | ||  || ||||||||||| ||||  || ||||||||||| || || | ||| ||||||| |||||||||||||||| | |||   |||||| | |||||||||   |||||||
------------------------------gtgagcggtcactgtggattagcattgtatttgagatg-taatgtattaattcacttgttttctatttgcagTTCTTTACCACTGTGCCCTATGCTTGTGAACCATCTAATTTACCAAAGTATCCTCCCACCAAAGAATTGGAT---ATAAAACTGAGAGATGAAAAAGCAAGAA

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|352795543|gb|FQ480131.1|FQ480131
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351046377|gb|FQ452993.1|FQ452993
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351055934|gb|FQ453395.1|FQ453395
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|352786901|gb|FQ481276.1|FQ481276
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351043417|gb|FQ451469.1|FQ451469
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351043887|gb|FQ452681.1|FQ452681
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351038967|gb|FQ457642.1|FQ457642
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351055161|gb|FQ440500.1|FQ440500
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351032086|gb|FQ460343.1|FQ460343
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351043841|gb|FQ452635.1|FQ452635
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGC
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|349824254|gb|FQ417641.1|FQ417641
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351013309|gb|FQ425014.1|FQ425014
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|352795551|gb|FQ480139.1|FQ480139
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|351034440|gb|FQ463253.1|FQ463253
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|352790536|gb|FQ478176.1|FQ478176
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT
EST: gi|352791008|gb|FQ480001.1|FQ480001
EST:     CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAA                         TTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAGGTGT
genomic: CAATTGATCCTGATGACCGAGGCACTGCCACTTCTGCTTTAAATAGTGAAgtgagtaatc ... ctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA
                                     ccttgtctctgctt  CT-rich tract
                      attgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctttagatctttagaaattggctcaatgtatacatttgaaaccgtgtagaactgctctgacttgattgtttacttggtaccttgtctctgcttacagTTCTTTACTACTGAACCATATGCTTGTGAGCCGTCAAGTTTGCCAAAGTGTCCTCCCACCAAAGAAATTGATGTAATAAAATTAAGAGATGAAGCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
ctgcttt
- - - - - - - -agaaatt
- - - - - - - - - - - - ctcaatg
- - - - - - - - - - - - - - - - - - - -tgaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - -actgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttgg