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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttctgggttttgtgtttctttcatccttgaatcttgggttggttttgattttccctcggcaacttggggttgtcttctct...

Basic information

species Vitis vinifera
transcript Vv19s0014g01160.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g44070.1 (Oryza sativa), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttctg--ggttttgtgtttctttcatccttg---aatcttg---ggttggttttgattttccctcggcaacttggggttgtcttctct
||||||||||||| || || || |||||||| ||| | | | |  | ||||| ||||||||||||||||| |||||||||||||| || || || || ||||      || |   |    |  ||  | |||  ||     | |   ||||   |  || |   | | | | |||   ||| | || ||  |  ||| | |       
AGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCAGCCTCCAGGTCGACGGCAAGGTCATCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAGAGgtaccccctggtgcacgcgctcgtgtagatttgttggaaaatgcgatcttggttagcctcgtttgctcgatattggggttctcgcg-cagttgcgggcttt-------

upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g54590.1 (Oryza sativa), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtg-atatttgcttttcctttttctgggttttgtgtttctttcatccttgaatcttgggttggttttgattttccctcggcaacttggggttgtcttctct
||||||||||||| || || || |||||||| ||| | | | |  | ||||| ||||||||| ||||||| |||||||||||||| || || || || ||||   ||    ||   ||||  |||     |   |   ||| |  | |||   |     | |||  ||  |       |      | |  ||| || ||  
AGTCCAAGTCCACCATCGGGGTCGAGTTCGCCACCCGCAGCATCCAGGTCGACGGCAAGGTCGTCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAGAGgtacgtacggcctcccccttcctctcctactctagccgcttcccgcgttggtgcgcaaatgggtagtgcatcgagtgtgttctgctagatttg-ctgctgg

upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G127648_T01 (Zea mays), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttc-tgggttttgtgtttctttcatccttgaatcttgggttggttttgattttccctcg-gcaacttggggttgtcttctct
||||||||||||| || || || |||||||| ||| | |   |  | ||||| ||||||||||||||||| |||||||||||||| || || || || ||||    | || | | |      | ||     |  || ||  | || | |   | | |  ||| |    | ||||    | ||  | |  | |||   |    
AGTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCAGTCTCCAGGTCGACGGCAAGGTCATCAAGGCCCAGATTTGGGACACCGCCGGCCAGGAGAGgtaccctctgatctgctccgaacgtgctcgcttcgtgtccgtgatgcattgctgtagatttgctccctactttcttgggagcctcctatgcttgatcttg--

upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G34410.1 (Glycine max), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttctgggttttgtgtt-tctttcatccttgaatcttgggttggttttgattttccctcggcaacttggggttgtcttctct-
||||||||||||| ||||| || |||||||| ||| | |||||||||||||||  ||| ||||||||||| ||||| |||||||| || || ||||||||||  |||||  ||  ||||   |      |||     ||   | |  |  | |  ||| |         |||    ||   | |      ||    |   | 
AGTCCAAGTCCACCATTGGCGTCGAGTTCGCCACCCGCACCTTGAACGTCGATTCCAAAGTCATCAAGGCCCAGATCTGGGACACCGCAGGCCAAGAAAGgttttatttttttccccttcccccccacattgcaagatcacgcttaatcaactaatggat--accccagtttcatgtcaaaagcccttcttttaaatggttg

upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA12G35970.1 (Glycine max), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttctgggttttg-tgtttctttcatccttgaatcttgggttggttttgattttccctcggcaacttggggttgtcttctct-------
||||||||||||| ||||| || |||||||| ||| | |||||||||||||||  ||| ||||||||||| ||||| ||||| || || || ||||||||||  | ||| |    | | |  |    | ||| |   || | | |  |  | |  |||||         |||    ||   |||      || ||||   |       
AGTCCAAGTCCACCATTGGCGTCGAGTTCGCCACCCGCACCTTGAACGTCGATTCCAAAGTCATCAAGGCCCAGATCTGGGATACCGCAGGCCAAGAAAGgt--tttttcccccccttctcccacattattgctagatcatgcttaatgaactaatgggt--accccagtttcatgtccaaaaccc----ttctctttaatggtggaa

upper sequence: Vv19s0014g01160.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G16920.1 (Arabidopsis thaliana), 5'ss of exon 1
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgt--gatatttgcttttcctttttctgggttttgtgtttc-tttcatccttgaatcttgggttggttttgattttc--cctcggcaacttggggttgtcttctct
|||| || ||||| ||||| || || ||||| ||  | ||||| || ||||||||||| ||| | || |||||||||||||||||||| ||||| || ||||  | | || |  || |   | |||   ||| ||  ||| | || |  ||| || |    | ||  || ||  |    || || |  ||    |||  ||    
AGTCTAAATCCACCATTGGCGTCGAATTCGCCACTCGTACCTTAAAAGTCGATGGCAAAGTCGTTAAAGCTCAGATTTGGGACACTGCTGGTCAGGAGAGgttcgtttttcgtcttcctcgtctcttcatttcgttcttcgtctcttatttgtatgtaaaatcggccttcatgctagatcttggta-tttcacattgagtt----

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|110692203|gb|EE071177.1|EE071177
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCCCTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|110727619|gb|EE104586.1|EE104586
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|37187555|gb|CF606908.1|CF606908
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCCCTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|110395262|gb|EC960920.1|EC960920
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|71866359|gb|DT015414.1|DT015414
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|110427396|gb|EC993833.1|EC993833
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|110686867|gb|EE063776.1|EE063776
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCCCTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT
EST: gi|110362941|gb|EC926504.1|EC926504
EST:     GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAG                         GTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCCCTCCT
genomic: GATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttg ... gacttaatagGTACCGAGCCATCACCAGTGCTTACTACCGAGGAGCTGTAGGTGCACTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCCAAGTCCACTATTGGTGTAGAGTTCGCTACCAGGACCTTGAACGTCGATGGCAAGGTCATCAAGGCTCAGATTTGGGACACTGCGGGTCAAGAAAGgtgatatttgcttttcctttttctgggttttgtgtttctttcatccttgaatcttgggttggttttgattttccctcggcaacttggggttgtcttctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccctc