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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttctttccttttttctgtttttctttgttgaaaaag

Basic information

species Vitis vinifera
transcript Vv19s0085g01130.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g48760.1 (Oryza sativa), 5'ss of exon 1
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCA---TTCGGGCAAGgtactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttctttccttttttctgtttttctttgttgaaaaag
   ||||||||| |  ||| | ||  ||||||||||  | ||||||||||||  | |||||  |||||||||||||||||||||||| ||     |   |||||||  |    | |||   ||  ||   |     ||||| | |   |   |||    |  ||||| ||   | |       |                   
---CCTGCTGGGGAAGTGGCGCGGGGAAGGCGAGGGGAGCTTCCCCACCATCTCCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacctcctcgc-ctgtatctgtatatctctttcgct--cgccaaagcttttaccttttctcgaccatgccgcacgcag----------------

upper sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G092152_T02 (Zea mays), 5'ss of exon 1
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTC---TCATTCGGGCAAGgtactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttcttt---ccttttttctgtttttc--tttgttgaaaaag-----------
   ||| ||||| |  ||| | ||  ||||||||||  | |||||||||||   |||||||   |||||||||||||||||||||||   |||| |   |||||          |||||  ||      || |||| |    ||  ||  |     ||    |    |||||    | |||| | ||  || |   | |  |     |           
---CCTACTGGGGAAGTGGCGCGGGGAAGGCGAGGGCAGCTTCCCCACCATATCCTCCTTCCGGTACGGCGAGGAGCTCCTCTTCTCGCATCATCCCTCCAAGgcgtgtggccctctctacctgcgatgtttctct-cgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcag

upper sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA15G42130.1 (Glycine max), 5'ss of exon 1
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTC---GGGCAAGgtactcctttttctctttc--taaatacttcctcttcttttgatgatgatgaagacgatgactt-ttttctttccttttttctgtttttctttgttgaaaaag
   ||| ||||||||||||||||||||||| || || || |||||||| ||||||||||||||||| ||||| ||||| | ||||||||||||     |||||||  |||| | ||| | ||  |||     ||        |||    |  | |  ||   |  || |||| ||||       | ||| | |    ||  |    
---CCTTCTGGGAACATGGAGAGGCCAAGGAGAAGGAGGGTTCCCCACTATCAACTCCTTCTCCTATGGCGAAGAGCTTCACTTCTCTCATTCCCCCAGCAAGgttttcctctctctttctccataatcgggtctctcaaagttgtctttttttattactgggttttattttgtttctagaccacagttatccaccattagag---

upper sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA08G17020.1 (Glycine max), 5'ss of exon 2
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTC---GGGCAAGg--tactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttctttccttttttctgtttttctttgttgaaaaag
   ||| ||||| ||||||||||||||||| || || || |||||||| ||||| ||||||||||| ||||| ||||| | |||||| |||||      |||||  |||  || | | |||   |||| |||  ||     | | |   |  |       || |||   || | |  | |||   |||||  ||| |  | |   
---CCTTCTGGGCACATGGAGAGGCCAAGGAGAAGGAGGCTTCCCCACTATCAATTCCTTCTCCTATGGCGAAGAGCTTCACTTCTCACATTCCCCCAACAAGgtttacctctctctttctgcataaacactatctgggtctctcaaagttctctcttttattactgggttttgttttgtttagagttttcttttttctagac--

upper sequence: Vv19s0085g01130.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G03880.1 (Glycine max), 5'ss of exon 1
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTC---GGGCAAGgtactcctttttctctttc--taaatacttcctcttcttttgatgatgatgaagacgatgact---tttttctttccttttttctgtttttctttgttgaaaaag
   ||| ||  | |||||||||| |||||| || ||| | |||||||| ||| | ||||||||||| ||||| ||||| | |||||| |||||      ||||||    || | ||| |||   |||| | |   |     | | |   |  |       || |||   ||||  |||  ||| || |||||| |  | |        
---CCTTCTCAGCACATGGAGAGCCCAAGGAGAAGGTTGCTTCCCCACTATCGATTCCTTCTCCTATGGCGAAGAGCTTCACTTCTCACATTCCCCCAACAAGgtttagctctctctttttgcataaacattatttgggtctctcaaagttctctcttttattactgggttttgttttgttttgttttgttttcccctctatt-----

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|110405725|gb|EC971272.1|EC971272
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAAGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|30251884|gb|CB969617.1|CB969617
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|30252290|gb|CB969841.1|CB969841
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|37190109|gb|CF609458.1|CF609458
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|30137494|gb|CB922832.1|CB922832
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|110386755|gb|EC951377.1|EC951377
EST:     AACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAAGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: AACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|26267560|gb|CA818623.1|CA818623
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT
EST: gi|29783196|gb|CB349218.2|CB349218
EST:     TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAG                         CCGGTGATTGCGTATAGCCAGAAGACTTGGAAATTGAGCTCCGGCGAGCCT
genomic: TCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactccttt ... gttgaaaaagCCGGTGATTGCGTATAGCCAGAGGACTTGGAAATTGAGCTCCGGCGAGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACCTGCTGGGAACATGGAGAGGCCAAGGCGAGGGTGGTTTCCCCACCATCAACTCCTTCTCCTACGGCGAGGAGCTCCTCTTCTCTCATTCGGGCAAGgtactcctttttctctttctaaatacttcctcttcttttgatgatgatgaagacgatgacttttttctttccttttttctgtttttctttgttgaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC