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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaacatggacttaaaggttcttccacatcagcttaggattgtctaaaattcatgtgggtttggacaaaggccataaattatttttatgttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGCTTGTCCTACTTAATGAATGACATGCCCCAAGAAGCTCTTGGGGATGCCA

Basic information

species Vitis vinifera
transcript Vv08s0007g01520.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01520.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G15830.1 (Glycine max), 3'ss of exon 9
ccaaacatggacttaaaggttcttccacatcagcttaggattgtctaaaattca-tgtgggtttggacaaa-ggccataaattatttttatgttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGCTTGTCCTACTTAATGAATGACATGCCCCAAGAAGCTCTTGGGGATGCCA
     |   |||  |      ||    |     |  |  | |   |||| |  | | | |  || |  |     | |||  ||||  || | |||| |  ||||||| ||||| ||||||||||| || || || |||||||| || |||||||| || || ||||||||||||||| | |||||||| ||||||||||| |
-gtgtctctgacagaggatacctatggccaagacaaataaataaataaattaaactctagcattagttacttatctatatcttatacttttttttttt-cagTTCATAGATGGAGGGACCATGGTGTCACCTACAGTGTATGCAAGACGCTGCTTATCTTATTTAATGAATGACATGGCACAAGAAGCCCTTGGGGATGCAA

upper sequence: Vv08s0007g01520.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G26690.2 (Glycine max), 3'ss of exon 6
-----ccaaacatggacttaaaggttcttccacatcagcttaggattgtctaaaattcatgtgggtttggacaaaggccataaattatttttatgttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGCTTGTCCTACTTAATGAATGACATGCCCCAAGAAGCTCTTGGGGATGCCA
     | | |||   |   |||      |  |||  |  ||| | || | |     | |  |  |||      |     |||  |   |||||  |||  |  ||||||| ||||| ||||||||||| || || || |||||||| |  |||||||| || |  || |||||||||||| | |||||||||||||||||||| |
gtggtctagacaaaaaa--aaattaagctatacaataagttatgtttttttgctggtga-ataagtt--acttatctatatatttgtgttttacatttgtttcagTTCATAGATGGAGGGACCATGGTGTCACCCACAGTGTATGCAATACGCTGCTTATCTTTATTGATGAATGACATGGCACAAGAAGCTCTTGGGGATGCAA
















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|110425902|gb|EC992297.1|EC992297
EST:     CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAA                         TTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
genomic: CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAAgtgagtaaaa ... ttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
EST: gi|34363245|gb|CF404830.1|CF404830
EST:     CCGCTTTCCGAGCTAAGGATTTCACANCTGCCATTGATTGCTACACCCAA                         TTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
genomic: CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAAgtgagtaaaa ... ttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
EST: gi|33410051|gb|CF215678.1|CF215678
EST:     CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAA                         TTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
genomic: CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAAgtgagtaaaa ... ttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
EST: gi|34544584|gb|CF512816.1|CF512816
EST:     CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAA                         TTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
genomic: CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAAgtgagtaaaa ... ttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
EST: gi|110364306|gb|EC923835.1|EC923835
EST:     CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAA                         TTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC
genomic: CCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTGATTGCTACACCCAAgtgagtaaaa ... ttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaattcatgtgggtttggacaaaggccataaattatttttatgttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGCTTGTCCTACTTAATGAATGACATGCCCCAAGAAGCTCTTGGGGATGCCA
 gtctaaa  putative branch site (score: 3)
                                     tttttatgttttct  putative PPT
                             ataaattatttttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaacatggacttaaaggttcttccacatcagcttaggattgtctaaaattcatgtgggtttggacaaaggccataaattatttttatgttttctgtagTTCATTGATGGCGGGACCATGGTATCCCCAACTGTGTATGCTAGGCGCTGCTTGTCCTACTTAATGAATGACATGCCCCAAGAAGCTCTTGGGGATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
ccaaaca
- - - - - - - - - - - - ccacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccataaa