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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgttggccctttttatcagtttaaaatttcaattcttacattacatcccctcccattatggttgcctgaggaaccttactttatctgtttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGATGGGGATGATGATGCTTCCAACTTTTTCTCG

Basic information

species Vitis vinifera
transcript Vv17s0000g06230.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G20860.2 (Glycine max), 3'ss of exon 5
-cctgttggccctttttatcagtttaaaatttcaattcttac--attacatcccctcccattatggttgcctgagga-accttactttatctgtttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGATGGGGATGATGATGCTTCCAACTTTTTCTCG
     | ||   |   |  || | |    ||  || |||||   |||| |||   | |       ||| ||| || |    |   | | ||      ||  ||||||||||||||| ||||||||||||||||      | ||  |||||| |||| |||  | | |    |  | ||||     
attcttgggaaataagtcccaatat----ttgtaaatcttatgtattaaatctttttcatggtcagtttccttagtatgtttgggtctgtcccaaaatttgcagTTAATGGCTCTTTTACTTCTGAGGCATGCTGCTCCCCTCTTCAATGCTGATGTGGAGAAAGCTATAGCATATTTTTAT---

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G33580.1 (Glycine max), 3'ss of exon 5
cctgttggccctttttatcagtt-taaaatttcaattcttacattacatcccctcccattatggttgcctgaggaaccttactttatctgtttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGATGGGGATGATGATGCTTCCAACTTTTTCTCG
  ||        |   |  | |  ||||||  ||  | ||| || |  | |        | |  |||  |   |    |   | | ||      ||  ||||||||||||||| ||||||||||||||||      | ||  |||||| |||| |||  | | |  |  ||  ||||| |  
-ttggaaagaagtcccagtattagtaaaatcacatgtattaaatcattttcatggtacatttccttggttttcgtgtttgggtctgtcccaaaatttgcagTTAATGGCTCTTTTACTTCTGAGGCATGCTGCTCCCCTCTTCAATGCTGATGTGGAGAAAGCT-TTAACATATTTTTAT--
















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|161714671|gb|FC062664.1|FC062664
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCACTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|71869682|gb|DT018737.1|DT018737
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|71869497|gb|DT018552.1|DT018552
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCACTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110685783|gb|EE062815.1|EE062815
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|32248014|gb|CD713833.1|CD713833
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110417057|gb|EC983083.1|EC983083
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|71871373|gb|DT020428.1|DT020428
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110376460|gb|EC941525.1|EC941525
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110400334|gb|EC966892.1|EC966892
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCACTGAACATCACCAATGCCGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110712693|gb|EE087960.1|EE087960
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGGCTGA
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCC-GA
EST: gi|110718657|gb|EE095738.1|EE095738
EST:     TGATACAAATGCCAGTGGAGCTGCCTTTTTGCCGCTCTGCGGCCCTAATT                         T-AATGGCTCTTCTACTTCTGAGGCA
genomic: TGATACAAATGCCAGTGGAGCTGCATTTT-GCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCA
EST: gi|110686225|gb|EE063635.1|EE063635
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCTGAT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGAT
EST: gi|110695017|gb|EE072554.1|EE072554
EST:     CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATT                         TTAATGGCTCTTCTACT
genomic: CTGATACAAATGCCAGTGGAGCTGCATTTTGCCGCTCTGCGGCCCTAATTgtaagccatt ... ttcttgacagTTAATGGCTCTTCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcccctcccattatggttgcctgaggaaccttactttatctgtttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGATGGGGATGATGATGCTTCCAACTTTTTCTCG
                             accttac  putative branch site (score: 3)
                                   ctttatctgtttctt  CT-rich tract
                                ttactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgttggccctttttatcagtttaaaatttcaattcttacattacatcccctcccattatggttgcctgaggaaccttactttatctgtttcttgacagTTAATGGCTCTTCTACTTCTGAGGCATGCGCTGAACATCACCAATGCCGATGGGGATGATGATGCTTCCAACTTTTTCTCG

cctgttg
- - - -gcccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctga