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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 6
gtgag---cctcttgaagattttattt---tattttattttta--ttattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
|| ||   || ||  || |       |   |||| | |||||   | ||  | ||||  ||   ||           ||    |||   || || |    |   ||  |    ||| |||| |||||||| |||||||||||| | || || || |||||||||  |||||||||||| || || ||||||||||| || ||| |||| ||| ||
gtaagacaccactgaaatacagcggctacatattgtgtttttggttcatcttcttttccttcactggcatgacaacctacttcatgttctgctg-ttgcactttttctctgatagGCATGTCTGGGAGTCCAAAGCTGATGGATCATTCGCTATCTCTGAGGATACATGGAATGAACCCCTGGGCCGTGGAACTGAAATAAGACTGCACCTCCGA

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 6
gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
            ||||  ||  |   | || ||||  | |||  ||  |||   | |  ||  | |    || |       |  || |  | ||      | || |||||||| ||||| || |||||||||||| | ||||| || |||||||||  ||||||||| || || || |||||||||||||| |||||||||||  ||
----------gtaagacattgctggctgtttttttgttcatttcttgatttacctatttacttgtgtcacatta-------ttgtggtgttgca----ctcttttagGTATGTGTGGGAATCAAAAGCTGATGGATCATTTGCCATCTCTGAGGATACATGGAATGAGCCCCTTGGCCGTGGAACTGAGATAAGATTGCATCTGCGA

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
                  | | ||     |  |  | || || ||  ||| |  | | |   |   | ||     | ||  |  || |  |  |      | || || ||||| ||||| || |||||||||||| | ||||| || || ||||||  |||||||||||| || || |||||||| ||||| ||||| |||||  ||
-----------------gtaagttaccgctgctgctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttggtgctgta----ctcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 6
gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggttta-tgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
                    | |   | || ||     |  |||  ||||| |||||  ||  |      |   |  ||  ||||  || ||||   ||||     |||||||||||||| || |||||||||||||| ||||||||||| || |||  |||||||||||| || || |||||||||||||| ||||| || ||||  
--------------------agtaagtctttttggacctgatatcgtttttgtttgttgacttgtaacccagctatctgacttgaaaattattcggttttc-----aGGTATGTATGGGAATCAAAAGCTGATGGAGCATTTGCAATTTCAGAAGATACATGGAATGAACCTCTAGGGCGTGGAACTGAGATTAGATTACACCTCAA-

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
gtgag-cctcttgaagattttattttattttatttttattattattt--------tttttttttgtgaaccagaggttta-tgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
|| || ||| ||| |  |  | || | |||    |   ||| ||||         ||||| |||||  ||  |      |      |   ||||   | |||    ||||     |||||||||||||| || |||||||||||||| || || ||||| || |||  ||||||||||||||| ||||| ||||||||||| ||||| || ||||  
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttc-----agGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG

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|110723753|gb|EE101423.1|EE101423
EST:     TTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGANCAA-CA                         GTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGNCA-TTTCTGAGGAT
genomic: TTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGA-CAAACAgtgagcctct ... ttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTG-CAATTTCTGAGGAT
EST: gi|30297571|gb|CB974365.1|CB974365
EST:     CTTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGACAAACA                         GTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGT
genomic: CTTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGACAAACAgtgagcctct ... ttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGT
EST: gi|110710305|gb|EE086522.1|EE086522
EST:     CTTGTTGCAGACTATGTTGAAGTCATTAGCAAACACCATGATGACAAACA                         GTATGTTTGGGGAGTCTAAAGCTGAAGGAGCTTTT
genomic: CTTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGACAAACAgtgagcctct ... ttccattcagGTATGTATGGG-AGTCTAAAGCTGATGGAGCTTTT
EST: gi|110709700|gb|EE085391.1|EE085391
EST:     TTGTTGCAGAAC-ATGTTGAAGTCCTTANCCAACACAATGATGACAAACA                         GTATGTATGGG
genomic: TTGTTGCAGA-CTATGTTGAAGTCATTAGCAAACACAATGATGACAAACAgtgagcctct ... ttccattcagGTATGTATGGG
EST: gi|110726118|gb|EE101621.1|EE101621
EST:     TTGTTGCAGAATATGTTTGAA-TCATTANCCAACACAATGATGACAAACA                         GTATGTATGGGAGTCTAAAGCCGATGGAGCCTTTG
genomic: TTGTTGCAGACTATGTT-GAAGTCATTAGCAAACACAATGATGACAAACAgtgagcctct ... ttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTG
EST: gi|110724805|gb|EE100952.1|EE100952
EST:     CCTGGTGCAGACTATGGTGAAGTCATTAGCAAACACA-TGATGACCAACA                         GTAAGTATGGGAGTCTTAAGCTGAAGGAACTTTTGCAATTTCTGAGGATGT
genomic: CTTGTTGCAGACTATGTTGAAGTCATTAGCAAACACAATGATGACAAACAgtgagcctct ... ttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA
                          gattgat  putative branch site (score: 4)
                                            tttccattc  putative PPT
               tttatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA