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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG

Basic information

species Vitis vinifera
transcript Vv01s0010g00950.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g10280.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttcttt-cattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
                                                                                                      | |  || ||   | |||  |||||  | |  |||||   ||      | ||    |   ||| | ||  ||||||| | ||   |        | | |||||||||||||||||||||| || ||||||||||| || |  || || |||||  | |||||||||||||| ||||
gtttgtgaaacatcttgagattgcaagtagtaaaagagttctgatttttttttctgtatatgtttaccgtatgcattgtgtttctaatatatccaaataaactggaaatcataatgcagttgttcatcaacttgattttatgaactatgctcctgccttgcatttgctttaatggtattgtattgtacc-----tttcctagACTTTTGATGCTGTTGATGGTAAACAAGCAAGGCGCACTAGCTCATCAAGTCCTCTAGGAGAACTTTTTGATCATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 4
-----------tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
           ||| |   |||  | |||   ||||||| ||||         | | |  | ||   |||| |||  ||         | || |   |          ||||||||||||||||| ||||| || ||||||||||| || || || || |||||  | || || ||||||||||| |
ggggttttcggttttcctggatctaatagc--ttcattttttattgaaatatcacgtcaatccttccatttttttagtttacatcgaatgttgtttatg---------cagACTTTTGATGCTGTGGATGGAAAACAAGCAAGGCGTACCAACTCATCAAGTCCTCTAGGCGAGCTTTTTGACCACG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
tttgctatgattgagtagtgtttcatttattatattttggcaat--gccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
|    |||   ||       |||  |  || ||   || |        |||| |||||| |  || ||||  | || ||| || |   |      |  | |||| |||||||||||||||||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||
tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgatt-catttattgt-tttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G14210.1 (Glycine max), 3'ss of exon 5
--tttgctatgattgagtagtgtttcatttattatattttggcaat--gccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
  |    |||   ||       |||  |  || ||   || |        |||| ||||||||  |||||||     |  |||| ||   |     ||  | |||| |||||||||||||| ||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||
catggtttattcatggaagacttttactacatgatgccttagtttccaatctttgctataatta-tttcattt---attcttttcttgtgtgtgtgcactctagACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 4
---------tttgctatgattgagtagtgtttcatt-tattatattt--tggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
         | |  | |  || |  ||| |  | || | |||||| |  |||  | |   |||  | | | | ||| ||  |    |  ||||   | |       |   |||| |||||||| ||||||||||||||||||||  |||||||||||||||| ||  | ||||| || || || ||||
gtttgcgtctctctttttcttcaaaagtttaactttctgttatatgtgctggtgaaggtgttttga-agtcttttttatctt--acaccttttgagcttt------tattagACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G25585.3 (Arabidopsis thaliana), 3'ss of exon 4
-tttgct--atgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG------------------------
 | ||||   |  ||   ||       | || | || |  | |  | |  |  | ||   | |||| |   | | ||   |   ||  | |   | || | |||| |||||||| |||||||||||||||||| |  | |||||||| ||||| ||| | ||||| |||||||||||||                        
gtctgcttcttttttctatatcaacctaatt-tcatctgcttgttaagggtcatgtaatctgtcttcctgacatagttggtgcattgtcgagtga-attctagACATTTGATGCGGTTGATGGGAAGCAAGCACGAAGAACAAATTCATCTAGCCCACTAGGAGAGCTTTTTGACCATGGTTGCGATGCACTTGGCTGTGCGT

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 3'ss of exon 4
tttgcta-tgattgagtagtgtttcatttattatatttt--ggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
 ||||   | |  ||  | |      |||    |  |||  ||  ||||  ||      ||       | ||    | | |   ||   |    |  |  ||||||||||||||||||||||| |||||||| ||||||||||| || || || ||  | ||||| |||||||| || |
attgccgctcaccgatcattacgatttttcgagtgatttaaggggatgcagttctgcccatacacccaagtcagaatgtctcaatt---tgtgtattttacagACTTTTGATGCTGTTGATGGCAAGCAAGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
----tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
     | |       || |   | | ||| ||     || | |     || ||   |||     |||    |   |     | |   ||| |    | |  ||||| |||||||||||||||||||| ||||| |||||||||||||| || |||||  | |||||||||||||| || |
ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacgg----ctctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG

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|351028084|gb|FQ425985.1|FQ425985
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|351043445|gb|FQ444045.1|FQ444045
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|37184688|gb|CF604042.1|CF604042
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|349829684|gb|FQ421202.1|FQ421202
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|349824351|gb|FQ417738.1|FQ417738
EST:     CACCAAGATGGGTGCACTTTGCCCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|110708043|gb|EE085132.1|EE085132
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|110694296|gb|EE071276.1|EE071276
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|351040557|gb|FQ434690.1|FQ434690
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|351014955|gb|FQ444244.1|FQ444244
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAACTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|351029069|gb|FQ435269.1|FQ435269
EST:     CACCAAGATGGGTGCACTTTGCCCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
EST: gi|110687900|gb|EE065836.1|EE065836
EST:     CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAG                         ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT
genomic: CACCAAGATGGGTGCACTTTGCTCATGGTTTACTTCTTTTCTTATACCAGgtttgtctaa ... aacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
                                      ccctaaa  putative branch site (score: 3)
       tataatttctttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgctatgattgagtagtgtttcatttattatattttggcaatgccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- -gctatga
- - - - - - - - - - - - - - - - - - - - caatgcc