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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC

Basic information

species Vitis vinifera
transcript Vv15s0048g02010.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 4
gtacttggaattg-atcttgatataccttgtgagcaat--tggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
|||  |    |   || |||  || |  | |    | |  | | | |   | || ||| || ||| |   |     | || || |    |||||   ||||  ||||| || ||| | ||||| || ||  | || || ||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||  ||||   | |||||||
gtatattatttcacattttgccattctgtatcgctactcctcgtcatgatggaaatttaca-atatttgggcataaagttattgaccagttattgatacaa-acagGCCAAGTGCTTGGAAACTGGAGAGACTGTTGCCATTAAGAAGGTTCTGCAAGATAAAAGATATAAGAACAGAGAGCTCCAAACAATGCAACTGCTTGACC

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 4
gtacttggaattgatcttgatatac-------cttgtgagcaattggcctttgggtaattttcc----agataatattgttctcattttt--ttat--gttttattttga---caatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
||| |||  ||| || |||   ||        || ||  | | |   ||||||  | | | | |     | | || | |||    | |||  ||||    ||   |||||    | || ||||||| ||||| ||||| ||||||||||| ||||| || || ||| |||| || |||||||| |||||||| ||||| ||  |||||||  | |||||||
gta-ttgatatttattttgcagtatttctttactcgtaggaattgatcctttgcttcactgttctatgggtttatctagttactttctttgcttatccacttcgctttgaatttactgtagGCTAAGTGCCTTGAAACTGGTGAAGCAGTTGCAATAAAAAAAGTGTTGCAAGACAAGAGATATAAGAATAGGGAACTGCAGGTTATGCGAATGCTTGACC

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
|||  ||||| |  ||||   ||| |  |     || |   | ||   || || |      |  |||       |   ||| ||| | |||||   |    |||| || ||||| ||||| ||||||  ||| |||||||||||||| ||||||||||| ||||||||||| |||||||| || || |||||  | |  ||||
gtaggtggaaat--tctt---atagcaggaacataactaatccttaactatttgtgttcccagaatt-------tgactttctgtctgatttttgga---tagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatg----cagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
       | | ||   | |  | || | |    ||  ||    | ||  | |  |   ||||  | |  |  ||| || | |||  |    |      ||    |||||||||||| | || |  || ||  | ||||| || ||||||||||| || || ||||||||||||||| |||| ||||| || ||| |  || | || |
------tgtactgtagtggtgaaacatgggatacatctgtttgtgggacactcatggtgatagaactaata-catattctcatgactgcggtgactcctgttgtcagGCTAAATGCATTGAGAGCGGGGAGACGGTGGCCATAAAGAAGGTGCTCCAAGACAAGAGATACAAGAATCGAGAGCTCCAGATCATGAGGCTATTGGATC

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctc--atttttttat-----gttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
 ||  |  | | || |  || ||     | |    ||  | |  |  || |  ||| || |  ||    |     || || | ||     |  | ||||||      ||||| |||||| |||| |  || ||| | ||||| |||||||||||||| ||||| ||||||||||||||  ||||||| || || |||||  | || || |
-taacttcactggagccagacat-----ggggctgatctgtccat--gtgacgttcaaggtggtagaactaggggatgttctgatcgcgagggtaattttgttg--tcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

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|349829752|gb|FQ421270.1|FQ421270
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|349828504|gb|FQ417246.1|FQ417246
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351029954|gb|FQ430696.1|FQ430696
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|349823414|gb|FQ423225.1|FQ423225
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351015296|gb|FQ445580.1|FQ445580
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351015511|gb|FQ447340.1|FQ447340
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|110713030|gb|EE088592.1|EE088592
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAN
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|352773646|gb|FQ472428.1|FQ472428
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|349817714|gb|FQ407703.1|FQ407703
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|161713339|gb|FC063356.1|FC063356
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351027217|gb|FQ444466.1|FQ444466
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351026191|gb|FQ428203.1|FQ428203
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|110712065|gb|EE089258.1|EE089258
EST:     CATGGCTGANGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAA                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAAGTGCTGCAG
genomic: CATGGCTGA-GCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|71856597|gb|DT005652.1|DT005652
EST:     GGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: GGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351025364|gb|FQ435056.1|FQ435056
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|34548045|gb|CF516277.1|CF516277
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
EST: gi|351021880|gb|FQ437667.1|FQ437667
EST:     ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAG                         GCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG
genomic: ACATGGCTGAGCGGGTGGTTGGCACTGGTTCCTTTGGGGTCGTTTTTCAGgtacttggaa ... gacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC
                                         ttttgac  putative branch site (score: 3)
         agataatattgttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA