Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgagctttaagcttgtatacatgagttgcggtcattttcttctggtgttatactaacaattttatttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC

Basic information

species Vitis vinifera
transcript Vv19s0014g01020.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 4
----gtacttgagcttta--agcttgtatacatgagttgcggtcattttcttctggtgttatactaacaattttatttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC---
    | |||| |  |  |     ||    | || | |        |||   | | |  |||   |     | ||  || |  ||| | || |||||||||||||||||||||||||| || || ||  | || || |||||||||||||| || ||   ||| || |   | |||||||||||||   
gtctgaacttcaattccactgctttagcaagataaatctttaatgtttgtgtttagcattaacatgtttgtattgctt-tggcagCTTCTCTACAGGAGGTACAGTGGAAATTTCCTAGTCAACCTTATTGGGAAATGGAAGGAATCTGAGTACTC---TGGCCATTCTGTTCCTGTTGGTGGTCTTG

upper sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 3
----gtacttgagctttaagcttgtatacatgagttgcggtcattttcttctggtgtta-tactaaca-attttatttct--tacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC---
      || | |  | |||   || |    | ||||      || ||||    |||| | | ||||   |||||| | ||   |||| | || ||||||| |||||||||||| |||||||| || ||  | || ||||||||||| |||||||| ||   ||| || |  || |||||||||||||   
gtacacacctcatttctaatgctgca---gtaagttat----atcttctgtatgtgtaactgctaatgtattttactgctatcacagCTTCTCTACAGGAAGTACAGTGGAAACTTCCTTGTTAACCTTCTTGGGAAGTGGAAGGAGTCTGAATACTC---TGGCCATTCTATTCCTGTTGGTGGTCTTG
















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|351031923|gb|FQ460180.1|FQ460180
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|33410560|gb|CF216187.1|CF216187
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|71867271|gb|DT016326.1|DT016326
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|71890402|gb|DT039457.1|DT039457
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTG
EST: gi|351035297|gb|FQ459564.1|FQ459564
EST:     CCATCATTCTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAG
EST: gi|161713522|gb|FC064063.1|FC064063
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351019144|gb|FQ429304.1|FQ429304
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351047982|gb|FQ441154.1|FQ441154
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|77577442|gb|DV217453.1|DV217453
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|349829390|gb|FQ419922.1|FQ419922
EST:     CATCATTCTACAGTCTGCTCTTTGTT-CCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAAATTTCCTTGTAAATCTCT
genomic: CATCATTTTACAGTCTGCTCTT-GTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAA-TTTCCTTGTAAATCTCT
EST: gi|156738579|gb|EV242700.1|EV242700
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|110717573|gb|EE093550.1|EE093550
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|110729814|gb|EE106178.1|EE106178
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|110403185|gb|EC964476.1|EC964476
EST:     TTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: TTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|30129932|gb|CB915271.1|CB915271
EST:     CCATCATTCTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351035066|gb|FQ458423.1|FQ458423
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|71865798|gb|DT014853.1|DT014853
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351054782|gb|FQ462812.1|FQ462812
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351048096|gb|FQ442066.1|FQ442066
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|30297202|gb|CB973996.1|CB973996
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAG
EST: gi|351053628|gb|FQ440137.1|FQ440137
EST:     CCATCATTTTACAGTCTGCTCTTGTTTC-AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGG
EST: gi|161714004|gb|FC063189.1|FC063189
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351024256|gb|FQ423679.1|FQ423679
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|110687837|gb|EE065701.1|EE065701
EST:     ATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: ATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|33403746|gb|CF209373.1|CF209373
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACCGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|71889203|gb|DT038258.1|DT038258
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|110361033|gb|EC924484.1|EC924484
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|33403829|gb|CF209456.1|CF209456
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|71868913|gb|DT017968.1|DT017968
EST:     CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: CCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351023126|gb|FQ432509.1|FQ432509
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
EST: gi|351029515|gb|FQ436909.1|FQ436909
EST:     AACCTTTACTTTATATCCCAG                         TTGCTGTACAGGAGATACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG
genomic: AACCTTTACTTTATATCCCAGgtacttgagc ... tttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgagttgcggtcattttcttctggtgttatactaacaattttatttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC
                               tactaac  putative branch site (score: 0)
                                        ttttatttctt  putative PPT
                            ttatactaacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgagctttaagcttgtatacatgagttgcggtcattttcttctggtgttatactaacaattttatttcttacagTTGCTGTACAGGAGGTACAGTGGAAATTTCCTTGTAAATCTCTTGGGCAAGTGGAAGGAATCTGAATATTCGGGTGGTCAATACATCCCTGTTGGTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG