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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccatttttagttgcacttttttctcttgttttagtagtataaactagatgatttgataacactaatttatgtgttttcacctctaacatggctttgctttcacag

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA02G04120.1 (Glycine max), 5'ss of exon 7
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacat----tcccatttttagttgcacttttttctctt----gttttagtagtataaa-ctagatgatttgataacactaatttatgtgtt----ttcacctctaacatggctttgctttcacag---
|| |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||||||||||||||||||||   |    ||||  |  ||  |||    | || | ||    | |  | || |||    |||  | |||   ||| |||  |  || | ||    || |  | |||||||   |||  ||    |   
TCTTAGAGATGAATCCTTTCACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTAGATGACACTGCTGCTTTCAAGAACTTCAAGAAgtgggttttttccctctagtaaatgccaagtgttattttcaaggatagaatattatctttctatttcattatgtaaaactggtggatattttgcggttaatatttaacatgtggttgaatttgttgtag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA01G03530.1 (Glycine max), 5'ss of exon 7
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccatttttagttgcacttttttctcttgttttagtagtataa-actagat---gatttgataacactaa-tttatgtgt-tttcacctctaacatggctttgcttt--cacag
|| |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||||||||||||||||||||   |||      |    |  |          |  ||| |    ||||| |||| ||    |||| ||||    ||  | |||  | |||  |  ||||||| | ||   |||     ||
TCTTAGAGATGAATCCTTTCACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTAGATGACACTGCTGCTTTCAAGAACTTCAAGAAgtgggttctttccctctagtaaatgccaagtgttattttcaaggatataatactatatttctatttcataatgtaaaactgatggatattttgcggctaacattggttgaatttgttgtag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA08G17010.2 (Glycine max), 5'ss of exon 7
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccatttttagttgcacttttttctcttgttttagtagtataaactagat----gatttgataacactaatttatgtgttttcacctctaacatggctttgctttcacag-------------------
|| | |||||||||||||| || |||||  ||||||||||||||||| |||| |||||||||||||| || |||||||||||||||||||||||||||||||   || |     | |     | | |   || || ||| |    |  | |  | ||     |||    |    ||| | |    | ||      ||| |    ||      ||                      
TCTTGGAGATGAATCCTTTCACTTTGGTCAATGGAAAGCCTTATCCTCTGGACATGAGAGGCGAGCTTGATGATACTGCTGCTTTCAAGAACTTCAAGAAgtgtgtttcttccctcaaa-ataatatcaactattatttgaaggatgaatatcatatctctaattcatcatgtataactgaataatgtttcatagtaaaagaatttataaaccatgcatgttattaatatttgcag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA15G42140.2 (Glycine max), 5'ss of exon 6
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccattttt-----agttgcacttttttctc------------ttgttttagtagtataaactagatgatttgataacact----aatttatgtgttttcacctctaacatggctttgct-ttcacag
|| | |||||||||||||| || |||||  ||||||||||||||||| |||| ||||||||||| || || || ||||||||||||||||||||||||||||   || |     |      | |  ||  | ||  |             |  | |   || |  |   |  || | |  ||||   |    | | || |  |||| |   |   ||||   ||  | ||  |||
TCTTGGAGATGAATCCTTTCACTTTGGTCAATGGAAAGCCTTATCCTCTGGACATGAGAGGCGAACTTGATGACACTGCTGCTTTCAAGAACTTCAAGAAgttggtttcttccctctaaagaatatcaactattatttgaaggatgaaaatcatatctctaattcatcatgtataactcaataatgttgcatagtataagaatttttaaaccatgcatgttattaatatttgcag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 8
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccattttt-agttgcacttttttctcttgttttagtagtataaactagatgatttgataacactaatttatgtgttttcacctctaacatggctttgctttcacag
| || |||||||| || |||||| | ||  ||      |||  ||| ||||| ||| | ||||||||||| |||||||||  ||| ||||||||| |||||||| |||  ||| || | || |  |    | |||    || |||  |      |  |   | ||  | || ||   || || || ||     ||| ||  | | |  ||||  
TGCTGGAGATGAACCCATTTACACTCGTCAATAACGTCCCTCTTCCATTGGACATGCGTGGCGAGCTGGATGATACTGCTCTTTTTAAGAACTTCCAGAAgtacgttctgattcttgaattactgtgaaatatctgacatttgtatca------atgttcgtagagcataccaacg-atttgcttaca-----aacgtgattcttcgctcac--

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|110363218|gb|EC926793.1|EC926793
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|110730830|gb|EE108354.1|EE108354
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTTCCA-TGCCATTTTGGAAAAGTTATGAGTCC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTT-CCAATGCCATTT-GGAAGAGTTATGAGTCC
EST: gi|71882514|gb|DT031569.1|DT031569
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|351054175|gb|FQ450257.1|FQ450257
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|71888760|gb|DT037815.1|DT037815
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|110730143|gb|EE106883.1|EE106883
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAGGAA                         GTGGGGCA-TATTGAATTTCCAATGCC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCC
EST: gi|110698225|gb|EE075525.1|EE075525
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCTAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|349822202|gb|FQ412466.1|FQ412466
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|110416323|gb|EC982295.1|EC982295
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|111125102|gb|EE253720.1|EE253720
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|71882170|gb|DT031225.1|DT031225
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|161718453|gb|FC065040.1|FC065040
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     GATATGAGAGGCGAGCTGGATGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
EST: gi|161714091|gb|FC064386.1|FC064386
EST:     GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAA                         GTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC
genomic: GATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattccc ... gctttcacagGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAGAGATGAATCCTTTTACATTGGTTGATGGAAAGCCTTATCCTTTGGATATGAGAGGCGAGCTGGACGATACTGCTGCTTTCAAGAACTTCAAGAAgtacattcccatttttagttgcacttttttctcttgttttagtagtataaactagatgatttgataacactaatttatgtgttttcacctctaacatggctttgctttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC