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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaaccaatattttgtttctcattttcaatgtcctggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT

Basic information

species Vitis vinifera
transcript Vv19s0085g00720.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g10784.1 (Oryza sativa), 3'ss of exon 5
------gttgaaccaatattttgtttctcattttcaatgtcctggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgct-tatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
       |   || |||   || ||| |       | | |  || |        ||| ||  |   |   |||  ||| |  | | || ||  ||  |   || |  || |     | |||||| ||||| ||||| ||||||||||||||||||||||||||||| || |||||||| ||||| |||||||| |||
gtacaaatgagacaaatggattttttttgtagcgaattattgtgctaccagcagtataagcac--gactctgtagttt-acttcacattctgcattcctaacacatactatggtgttaacagACTGATCTTCTAGTGGCTGCTGCCAAGACTGGAAAAATTATCAACATCAAGAAAGGACAATTCTGTGCTCCTTCT

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 6
-------gttgaaccaatattttgtttctcattttcaatgtcctggtg-attctgttatgaggtccaaagagtgtgttttgatc-tgatatgcttatctcattcaaagtctct--tacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
        |||||| ||    || | | |      || | |  |  |  |||     ||||  | |||   |  | |||  | | || | ||  | | | ||  |||     |  ||  ||||||||| ||||| ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||| ||||| || |||
gtacagttttgaacaaaagaattttctgtggacaccagttttttcatatatttaagcatgac-tgcaatctgcatatttgtaccatgttctgaatctttaatgtaaacatattactatgatgacagACTGATCTTCTAGTGGCTGCTGCTAAGACTGGAAAAATTATCAATATCAAGAAAGGACAATTCTGTGCGCCTTCT

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 5
gttgaaccaatattttgtttctcattttcaatgtcc-tggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT-
  | ||    ||||   ||   || ||||||| ||| |  | ||| | |  | |       |     |||    |  | |     |||| |||||||   | | |   |||||||||||||||| ||||| || || ||||| ||||| ||||||||||| |||||||| ||||| || |||||||| ||| 
--taaatatctattgcatt---caatttcaatatccattataattttctggttaaaattttaatagatgtgccaacttcaa----ttatttcattcattttatttc-taatgacagaCAGATCTTCTAGTTGCAGCAGCCAAAACTGGGAAAATTATCAACATTAAGAAGGGCCAGTTCTGTGCTCCTTCTG

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 6
gttgaaccaatattt-tgtttctcattttcaatgtcc-tggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
        ||| ||| |     ||| ||||||| ||| |  | ||    |  | |      || ||  |||    |  | |     |||| ||||| ||  |  |||   ||||||||||||||| ||||| || || ||||| ||||| ||||||||||| |||||||| ||||| || || ||||| |||
-----gtaaatgtttattgcattcaatttcaatttccattataataggctggttaaaatttaatag-atgtgccaacttcaa----ttatttcatt-aattttgcttcttatgacagACAGATCTTCTAGTTGCAGCAGCCAAAACTGGGAAAATTATCAACATTAAGAAGGGCCAGTTCTGCGCTCCTTCT

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G79500.5 (Arabidopsis thaliana), 3'ss of exon 5
gttgaaccaatattttgtttctcattttcaatgtcctggtgattctgttatgaggtccaaagagtgtgttttgatctga--tatgcttatctcattcaaa--gtctcttacaatg--acagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
  |||  |  ||   ||| | |  |  |||| |   | |    |   ||   |  |    |   ||  ||   |||||   |||| ||   | ||| ||   ||   ||  |||   |||||||||||| || || || || ||  | || |||||||||||||||||||||||||| ||||| |||||||| |||
-gtgagactctaaactgtattt--tcctcaaagcttttgattgtagctttcaaactgtcgatcttggattgatatctgttctatggttga-tgatttaagttgttaattgtaattccacagACAGATCTTCTGGTTGCAGCAGCACAAACCGGAAAAATTATCAATATTAAGAAAGGACAATTCTGTGCTCCTTCT

upper sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G16340.4 (Arabidopsis thaliana), 3'ss of exon 5
------gttgaaccaatattttgtttctcattttcaatgtcctggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
       |  |||  ||  |||  |||   | ||   |  |      ||| |  | |   ||   ||       |||  || |     | | |     || |   |  | || |    ||||||||||| || ||||| || ||| | | ||| ||||||||||| || |||||||| |||||||||| || ||||
gcaagattctaacatatgcttttcttcaactcttttttagctatcaaattttcatttactgtttgaatttatcattt--atatacagagttcagggttttaactattgcctatatctccagACAGATCTTCTGGTCGCGGCAGCCCAAAGTGGGAAAATTATCAACATAAAGAAAGGACAATTTTGTGGTCACTCT

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|110708160|gb|EE085385.1|EE085385
EST:     TTGGCAGAGTTGCAGACATCATTCAGATTCCAGCTTTCCTCTGTCGTCAG                         ACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAG
genomic: TTGGCAGAGTTGCAGACATCATTCAGATTCCAGCTTTCCTCTGTCGTCAGgttgaaccaa ... acaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAG
EST: gi|30252416|gb|CB969967.1|CB969967
EST:     TTGGCAGAGTTGCAGACATCATTCAGATTCCAGCTTTCCTCTGTCGTCAG                         ACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAG
genomic: TTGGCAGAGTTGCAGACATCATTCAGATTCCAGCTTTCCTCTGTCGTCAGgttgaaccaa ... acaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT
                                        ctcttac  putative branch site (score: 3)
                                       tctcttac  CT-rich tract
        ttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaccaatattttgtttctcattttcaatgtcctggtgattctgttatgaggtccaaagagtgtgttttgatctgatatgcttatctcattcaaagtctcttacaatgacagACAGATCTCCTAGTCGCTGCTGCCAAGACTGGAAAAATTATCAATATTAAGAAAGGCCAATTTTGTGCTCCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA