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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaacttagagatttagatttaaaaaatgcttttgtgatcctgttaattaacttgaaacttgaacctgtcaaccatgtatgccattatctgcttc...

Basic information

species Vitis vinifera
transcript Vv00s0187g00380.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G062416_T04 (Zea mays), 5'ss of exon 1
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaa--caacttagagatttagatttaaaaaatgcttt--tgtgatcctgttaatta-acttgaaacttgaacctgtcaaccatgtatgccattatctgcttc
|||| || ||  | || ||||||||||| |||||||| ||  |  |||| ||| |||||||  | ||||| ||||| ||||||||||| ||||| |||||||||    | ||||       |   ||     ||||||||  | ||||  ||| |  |  |    |    |   | ||||    ||  ||   | || | |||| 
AGTACCAGTTCAGTCAATATGCATGGACTCACATGATCCTTCTCATGGTATTTGCCCAGTCATCTTTCACTGTGGCAAACATTTTTGATGGAATATTCTGgtaagcttctactttacagcatgcttt-----aatgctttgatctgatagtgtaatctggatgccagtggtatgcttgtctgatatagataggaataccagctta

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G32660.2 (Glycine max), 5'ss of exon 5
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaacttagagatttagatttaaaaaat---gcttttgtgatcctgttaattaacttgaaacttgaacctgtcaaccatgtatgccattatctgcttc
|||| ||||||||||||||||| ||||||||||||||||||||||| || |||  ||||||  ||||||||||||| | |||||||||||| |||||||||||| | ||| || | |   | ||    |  ||    |  || ||||      || |  |   |   ||  |    ||     || |||  || || |     
AGTACCAATTTGGCCAGTATGCTTGGACACACATGATTCTAATTGTTGTATTTGGCCAGTCCTCCTTCACCGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataacctataaaaggaaatgatgattatttaacaattatgataaaaaaaaattgcactactttttgaggattctcttttgcatgaaatcatatca---

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 5
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaacttagagatttagatttaaaaaatgcttttgtgatcctgttaattaacttg----aaacttgaacctgtcaaccatgtatgccattatctgcttc
|||| ||||||||||||||||| ||||||||||||||||||||||| || |||  ||||||  ||||||| ||||| | |||||||||||| |||||||||||| | ||| ||   |   | ||    |  ||  |||     |  || |||  ||  ||    | | ||  |    |      || |||  || || |  |  
AGTACCAATTTGGCCAGTATGCTTGGACACACATGATTCTAATTGTTGTATTTGGCCAGTCCTCCTTCACTGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataacctatgaaaggaaat---gatgattatttaactcttatgctaaaaaaactgcactacattttgaggattttcttttgcatgaaatcatatcatg-

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 5'ss of exon 4
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgta-------aaacaacttagagatttagatttaaaaaatgc---ttttgtgatcctgttaattaa-cttgaaacttga-----acctgtcaa-----ccatgtatgccattatctgcttc-----
| ||||| ||| |||| |||||||||||||| |||||  |||||||||||||||| |||||  | ||||| || |||||||| ||||||||||| ||||||||       |  |   |||  | ||   | ||      | |   ||| ||  |  ||||| ||   |||| | ||||      ||||| | |     | || ||    | |   ||||       
AATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCAGTCCTCATTCACTGTCGCCAACATCTTTGAAGGAATCTTCTGgtagtcacctattccttttaacgcttcttacttgtttgctccgtgtttagttcttgtgttattttctcttgtatcttggttatgacctgactaaaagtctatttactatactggttgctggtgcag

upper sequence: Vv00s0187g00380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaacttagagatttagatttaaaaa----atgcttttgtgat--cctgttaattaacttgaaacttgaacctgtcaaccatgtatgccattatctgcttc
|||| || |||||||||||||| ||||| ||||||||  | || || |||||||| || ||  | ||||| || |||||||| |||||||| || |||||||| |   | |||   || |     ||  ||    ||||||||  ||      ||  ||||| ||       ||| |         | | || ||  |  |     
AGTACCAGTTTGGCCAGTATGCTTGGACCCACATGATCTTGATAGTCGTGTTTACTCAATCGTCGTTCACTGTTGCCAACATATTTGAAGGGATCTTCTGgtacac--atttaataatgtcaccatatgaagtttatgctttttcgactattcgtatattaagtttgctaaggaatcatctttttctatttgtcaccacatt----

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|30327030|gb|CD010292.1|CD010292
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
EST: gi|32271292|gb|CD720451.1|CD720451
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
EST: gi|30324235|gb|CD007497.1|CD007497
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
EST: gi|32249237|gb|CD715056.1|CD715056
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
EST: gi|32271411|gb|CD720570.1|CD720570
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
EST: gi|32249768|gb|CD715587.1|CD715587
EST:     TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTG                         GTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT
genomic: TTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaac ... atcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCAGTCTGCCTTCACCGTGGCCAACATTTTTGAAGGAATTTTCTGgtaaaacaacttagagatttagatttaaaaaatgcttttgtgatcctgttaattaacttgaaacttgaacctgtcaaccatgtatgccattatctgcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat