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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA

Basic information

species Vitis vinifera
transcript Vv13s0019g01900.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgtt-acatgttcttttatgttgtt-tcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA
        |  |||  |  ||  | |||| |  || || ||| ||    || |||| |  || | | |||   |   || |||   | ||  ||||||| || ||||||||||| || ||||||||||| ||||||||||||  ||| || || || ||||| || ||  |  |
---gtataaaacttctaaattcttattgctagctcgtt-ctgattct--ttcaaagattttgctgatatggagtgacatattggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g38370.3 (Oryza sativa), 3'ss of exon 3
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgtt-acatgttcttttatgttgtt-tcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA--------------------
        |  |||  |  ||  | |||| |  || || ||| ||    || |||| |  || | | |||   |   || |||   | ||  ||||||| || ||||||||||| || ||||||||||| ||||||||||||  ||| || || || ||||| || ||  |  |                    
---gtataaaacttctaaattcttattgctagctcgtt-ctgattct--ttcaaagattttgctgatatggagtgacatattggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAGTCTGTTGCTATTTCTCCTA

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 3'ss of exon 5
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttc-ctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA
|| |||  ||    || | |   |  | |  |||  |   | |   ||   |    ||  ||| ||    |  | |||  |||        ||||||| ||||||||||| ||||| ||||||||||| || || || |||||||| ||||| || ||||| || ||  ||||
gtaaatggatga--actgttcgctagttcattatgatcaatagcccaaacagttcttttgctgataatactgttgttaaattggacacctgagGTTGGAGAGGTTGCAAAGATCACATGCAAGCCAGAATATGCTTATGGAGCTGCAGGTTCACCTCCAGAGATACCGCCAGA

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 2
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgttacatgttcttttatgtt--gtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA
                |  |  |  ||  | | |||    | |          |  |   ||| ||||| |||   || |         |  ||||||| |||||||||||||| || |||||  |||| || ||||| |||||||| || || |||||||| || ||| |  |
--------------gtatgtcaacgtttgcgtctctcgctttggcctttcaccatctctgtgtgacatggtctggcatatccaaaaaaattaagGTTGGCGAGGTTGCAAAAATTACATGCAAATCAGAATATGCATATGGAGCTGCAGGCTCACCACCAGAGATACCTCCTAA

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA
     ||||      ||   || |  ||  |  | | ||    | || |||   | ||  |  | ||||  ||| | || |  || | ||||||||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| ||||
----gtctaacaaagcaaacttttgatgaaac-tatatttaaataaaggttttcaattttttct-catg--cttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
gttaatctattcttacagctttatcttgccat---atcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA-
 |  | | ||  | |||     | |||   ||   |   | | ||  ||| | |      |  | |  ||||  ||| | || |  || | ||||||||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| |||| 
-tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatg--cttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG

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|28967033|gb|CB346066.1|CB346066
EST:     GGAAAGG-ACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|110366799|gb|EC930717.1|EC930717
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|71877473|gb|DT026528.1|DT026528
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|351029576|gb|FQ427416.1|FQ427416
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|351024603|gb|FQ433018.1|FQ433018
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|22015347|gb|BQ800381.1|BQ800381
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|77587550|gb|DV222939.1|DV222939
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|110376394|gb|EC941458.1|EC941458
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|110415144|gb|EC981021.1|EC981021
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|28967261|gb|CB346294.1|CB346294
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|110417551|gb|EC983617.1|EC983617
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|110422056|gb|EC988368.1|EC988368
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
EST: gi|30302283|gb|CB979077.1|CB979077
EST:     GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAG                         GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT
genomic: GGAAAGGCACTGTAATTAAGGCATGGGACATTGCTTTGAAAACAATGAAGgttaatctat ... tttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA
                                ttcttttatgttgttt  CT-rich tract
                                ttcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgttacatgttcttttatgttgtttcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG