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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaatctccgagcctgaggtataggtccaaatctttgtcaagcaaatttattttatcttgttaatatttcgaatgatgaatcatattcagttaaactgaagcttcttttgtagttttgttattttgttccataggtttgcttaaaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG

Basic information

species Vitis vinifera
transcript Vv15s0046g00180.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g02450.2 (Oryza sativa), 3'ss of exon 4
gtaattaatctccgagcctgaggtataggtccaaatctttgtcaagcaaatttattttatcttgttaatatttcgaatg-atgaatcatattcagttaaac-tgaagcttcttttgtagttttgttattttgtt----ccataggtttgcttaaaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG
                                                         |||  | |  | |||| | | | ||| |  |   |     || |  |||    |  ||| | | ||   | |  |      | | || |    ||  ||||    |      ||  ||||||||||||| ||||||||| ||||||| |||||||| ||||  |||    | ||||| |||||||| ||  | || || ||  | ||||| |||
--------------------------------------------------------gtatgatatagagatttgggacggatggagtagggttcacgaatcacgaaagaacaattgcattattacaactgcgaaatgactacagatgaatttctaactttgttt--gccttgcagATATGTTGGTACTTTACTGACACTTGGGAACAATTCCGTATCAGCGGATTCATAGATGTGATTGATGGTTCAAACCCCGAACCTGTCAAGCTACAG

upper sequence: Vv15s0046g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G02580.2 (Glycine max), 3'ss of exon 3
gtaattaatctccgagcctgaggtataggtccaaatctttgtcaagcaaatttattttatcttgttaatatttcgaatgatgaatcatattcagttaaactgaagcttcttttgtagttttgttattttgttccataggtttgctta--aaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG
                                                                                       || | | |  |   |   ||| ||||       | || |  |    | ||| |||    |  ||  |||  |||   | || |||||||||||||||| || || || ||||||||||| ||||| |||||    || ||| | |||||||| | | ||||||||||  | || ||||||
--------------------------------------------------------------------------------------gtaattattccatgaggtactttttttaataaaattttgtgatcgggcgtagattttgagactaagttcagttctttcggtt-agATATGTTGGTATTTCACAGATTCCTGGGAGCAATTTCGGATAAATGGGGATGTAGATATCATTGATGGTTTGAATCCTGATCCGCTAAAACTTCAG

upper sequence: Vv15s0046g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G46580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattaatctccgagcctgaggtataggtccaaatctttgtcaagcaaatttattttatcttgttaatatttcgaatgatgaatcatattcagttaaactgaagcttcttttgtagttttgttattttgttccataggtttgcttaaaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG
                                                             |    |||  || | || ||  || ||          |  ||||  || |  || | ||  || |  |||      ||||              || |  |     |||| |||||||||||  | ||  ||||||||||||||||||||||||||||  |||| || |||||||  ||  ||||||| |  |  |||||||||
------------------------------------------------------------gtaagaaattatttggattatacattatg--------gatcgaagaatcatgcgttgattgattctactgtggtggtggtt--------------gttttttccccaagATGTGTTGGTATTTCTCGGATACTTGGGAGCAATTCCGGATCAATGGAAGAATTGAGGTCATTGATGCGTCCAATCCTGACCAGACCAAGCTTCAG

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|34415057|gb|CF413811.1|CF413811
EST:     CTTAAGCATTGCCCATTTTCCGAG                         ATATGTTGGTATTTTACTTACTCTTGGGAGCAATTCCGGATCAATGGAAGG
genomic: CTTAAGCATTGCCCATTTTCCGAGgtaattaatc ... aatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGG
EST: gi|110412945|gb|EC978712.1|EC978712
EST:     ATTGAAGAGCTTAAGCATTGCCCATTTGCCGAG                         ATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGG
genomic: ATTGAAGAGCTTAAGCATTGCCCATTTTCCGAGgtaattaatc ... aatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGG
EST: gi|110730732|gb|EE108144.1|EE108144
EST:     ATTGAAGAGCTTAAGCATTGCCCATTTTCCGAG                         ATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGG
genomic: ATTGAAGAGCTTAAGCATTGCCCATTTTCCGAGgtaattaatc ... aatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttttgttattttgttccataggtttgcttaaaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG
                                         gtctaat  putative branch site (score: 3)
     ttgttatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaatctccgagcctgaggtataggtccaaatctttgtcaagcaaatttattttatcttgttaatatttcgaatgatgaatcatattcagttaaactgaagcttcttttgtagttttgttattttgttccataggtttgcttaaaactcaagtctaatgttttagATATGTTGGTATTTTACTGACTCTTGGGAGCAATTCCGGATCAATGGAAGGGTTGATGTTATTGATGGATCGGATCCTGATCCCATGAAGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC