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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagccgattgcagtgttcccgttctgttttttttcttgctaatagttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC

Basic information

species Vitis vinifera
transcript Vv09s0002g02590.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os01g51040.1 (Oryza sativa), 3'ss of exon 14
ttgagccgattgcagtgttcccgttctgttttttttcttgctaatagttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC
      |  | ||||| ||     | | | ||  |  | | ||    | | |  || |       |  |||| | |||        | ||     || ||||  || |  | ||| | || || || |||||| | |||||||| ||  | ||||||| |||||| ||||||||||| ||||||||||| ||||| ||||
---gttcattagcagtttttttaatatatattcctcatagatatacttgcatgtctcatgccttgtaatactca-atgtgaaaaattctt-----ttcagTTCTTGGTTGTTATGGCAATCTGTACAAACTGCTTGCTTCTTGTTTGTCTGTATGATGAGGAGGGTAAATGGAAAATTGAGCCAGGACTGGCAGCCATCC

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G091494_T01 (Zea mays), 3'ss of exon 14
ttgagccgattgcagtgttcccgttctgttttttt-tcttgctaatagttcgtcactt-aacatcaatcttactgagatggccctgtctgttggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC
              || | |  | |    |||||  | |  ||| | ||  ||      || ||  || |  ||||  |  | |||    |||   ||| ||||  || |  | ||| | ||||||||||||||| | ||||| || ||  | ||||| | ||||||||||||||  || ||||||||||| ||||||||||
--------------gtttactagctgaactttttaatttcactacttgtgagttgtgggaatatgcatgtc-ctgat-tcactctgaagtttgt--tttcagTTCTTGGTTGTGATGGCAATATGCACCAACTGCTTGCTTCTCGTTTGTCTGTATGACGAGGAGGGGAAATGGAGGATTGAGCCAGGACTAGCAGCAATCC

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA07G01550.1 (Glycine max), 3'ss of exon 14
-----------------------------------------------------------------------------------ttgagccgattgcagtgttcccgttctgttttttttcttgctaatagttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattt-tagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC
                                                                                   || | |  ||  |    |    |       | | | |    | |  |||   ||||| |  |  || | |||   ||         |  |  | ||| |||||||| ||| | ||||| ||||||||||||||||  ||| | | |||  ||||||||| |||||| ||||||||||||||||| |||||||| |||||  
gtatttatttatatattttggaaggtgcttgtcaattattttgcataatccacttcatattaattataaattggaaaaacatgtttaccaaataaccaactatatggaagagatatctacaccttga--gttatacacttgatttttatataactctaatttaagaacattcttcattttgtagTTTCTTATATTGATGTCTATATGCACCAACTGCGCTCTTTTAGCATGGCTATATGATGAGGAGGGAAAATGGAAAATAGAGCCTGGACTTGCGGCAATAT

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G20980.2 (Glycine max), 3'ss of exon 14
-----------------------------------------------------------------------------------ttgagccgattgcagtgttcccgttctgttttttttct-tgctaatagttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattt-tagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC
                                                                                       |   |    |       |  | ||     | |||   | |  | ||   ||||| |  |  ||   |||   ||         | ||  | |||  ||||||| ||| | ||||| |||||||||||||| |  ||| | | |||  ||||||||| |||||| ||||||||||||||||| ||||||||||||||  
gtatttatttatatatacagactttggaaggtgcttgtcaattatttttgataatccacttcagattaattataaattggaaaacatgttcaccaaataaccaactatatggaagatatctacaccatgaattatacacttgatttgtatacaactctaatttgagaacatttttcattttgcagTTTCTTATACTGATGTCTATATGCACCAACTGTGCTCTTTTAGCATGGCTATATGATGAGGAGGGAAAATGGAAAATAGAGCCTGGACTTGCAGCAATTT

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|352782051|gb|FQ469349.1|FQ469349
EST:     CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAG                         TTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
genomic: CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtct ... ggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
EST: gi|352777746|gb|FQ466799.1|FQ466799
EST:     CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAG                         TTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
genomic: CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtct ... ggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
EST: gi|110687623|gb|EE065247.1|EE065247
EST:     CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAG                         TTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
genomic: CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtct ... ggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
EST: gi|110392205|gb|EC957460.1|EC957460
EST:     CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAG                         TTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
genomic: CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtct ... ggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTA
EST: gi|110698301|gb|EE075671.1|EE075671
EST:     CGGTTCCTCGTGCTGCTGCAAAAATTGGAGCTGGGCTTAA-ATCTTTCAG                         TT-CTGATAA-AATG
genomic: CAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACATCTTTCAGgtatttgtct ... ggaattttagTTTCTGATAATAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC
                   atcttac  putative branch site (score: 3)
                                               aatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagccgattgcagtgttcccgttctgttttttttcttgctaatagttcgtcacttaacatcaatcttactgagatggccctgtctgttggaattttagTTTCTGATAATAATGTCGATATGCACCAACTGCGTACTTCTTGTATGCTTATATGATGTGGAGGGGAAATGGAAAATAGAGCCAGGACTTGCAGCAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - -tgttccc
- - - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg