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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcccaaattctacaaatgaatcttttccatggctgaatcctgaaaaatacaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 8
gcccaaattctacaaatgaatct---tttccatggctgaatcctgaaaaat--acaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA
     | | | |||  | ||| |    || ||    ||  |||  ||  |   | || || | |     |  |  |||  ||     |    |||     ||||||| |||||||||||| ||||||| |||||  |  | ||||| || || || ||||| |||||||| |||||||||||||||||||||||||| || ||||
-----agtcccacagctcaatataacatttcaattttgcttccctaatgactgataaattccttggtcatagaaaattcattactgagtccttttgatctttcagGTTATTGGAATTGATTTGCTGTCACAATCACTGTTACCGGCGATCGTAGAACTTGCAGAGGATAGGCACTGGAGGGTTCGGCTTGCAATAATTGAGTACA

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
----------------------------------------------------------------------------------gcccaaattctacaaatgaatcttttccatggctgaatcctgaaaaa---tacaattttcattagtgttcagt-atttcttttcatgcatattttt-ctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA
                                                                                  ||      |    |    |   ||||  | |      ||||  |||    | |  || || | |   ||   | ||   |  | ||   | ||||     ||||||| |||||||||||  |||| ||||||||  | || || || ||||| || ||||| |||||||| |||||||| || |||||||||||||| || ||||
gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 8
-gcccaaattctacaaatgaatcttttccatggctgaatcctgaaaaatacaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA
 |   |   | |     | ||  | |      | ||  |||||  |      | ||   | | || |     | |   |||   | | | ||| | ||||||| |||||||||||  || |||| |||||  | ||||| |||||||| |||||  |||| ||||| |||||||| ||||||||||| ||||| || ||||
agaataggctttttttttaaacttgtgttcaagatgtttcctggcatcattcacttcattcaatgatgtacttgtaagttctctcctgtattttt-ttcagGTTATTGGAATTGACTTGTTGTCGCAATCACTTCTGCCAGCCATTGTAGAGCTCTCTGAAGATAGGCACTGGAGAGTTCGGCTTGCCATAATTGAGTACA

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
----------------------------------------------------------------------gcccaaattctacaaa--tgaatcttttccatggctgaatcctgaaaaatacaattttcattagtgttcagtatt-tcttttcatgcatatttttctg----ttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA
                                                                        |||  |  ||  |   || |  ||||  | | |    ||||| ||        |  |  |       |||  | |   ||  || || || || ||    ||||||| ||||| |||||  |  | || ||| |  | || || |||||||| || ||||| |||||||| |||||||| || |||||||||||||| || ||||
gtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA

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|349825185|gb|FQ415732.1|FQ415732
EST:     CAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: CAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|22012824|gb|BQ797858.1|BQ797858
EST:     TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|110691608|gb|EE069902.1|EE069902
EST:     TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|22012767|gb|BQ797801.1|BQ797801
EST:     TTCCTGATGTCCGACTGAATATTATCAGCAAGC-TGATCAAGTAAACCAG                         GTGA-TGGAA-TGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|351031302|gb|FQ445327.1|FQ445327
EST:     CAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: CAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|71866595|gb|DT015650.1|DT015650
EST:     TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|110428387|gb|EC994857.1|EC994857
EST:     TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: TTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
EST: gi|110411876|gb|EC977604.1|EC977604
EST:     CAGCAAGCTTGATCAAGTAAACCAG                         GTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG
genomic: CAGCAAGCTTGATCAAGTAAACCAGgtttgtctga ... ttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA
                                          tttttctgttc  CT-rich tract
     aattttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccaaattctacaaatgaatcttttccatggctgaatcctgaaaaatacaattttcattagtgttcagtatttcttttcatgcatatttttctgttcagGTGATTGGAATTGATCTGCTGTCTCAATCCTTACTGCCGGCCATTGTTGAGCTTGCTGAGGATAGACACTGGAGGGTTCGGCTTGCAATAATAGAATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
-cccaaat
- - - - - - -aaatgaa
- - - - - - - - - - - - - ccatggc
- - - - - - - - - - - - - - - - -tgaatcc
- - - - - - - - - - - - - - - - - - - - - aaaaata