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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgtttcctgtggaaagtcttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG

Basic information

species Vitis vinifera
transcript Vv11s0206g00130.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
gttttgtttcctgtggaaagtc-ttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatat----agAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG
      | | | || ||   || ||||   | |  ||||  |      | |   || | |  ||  | || | | | | |      || |   | ||||    |||||| || || || ||  ||||||| ||||||||||| ||| | |  ||||||||||| ||||||||||| ||||| ||||||||  | || ||  ||
----aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtca-tgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 1
---gttttgtttcctgtggaaagtcttttgtatgttttga-tatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG
       | |  |          |  |||| |  ||| || ||  || ||||       ||| |   ||    |     |||   | |  |  | |||    ||||||||| || || ||  ||||||||||||| ||||||||  |||  ||||||||||| ||||||||||| ||||| ||||||||  | || || |||
cataacatatggctgaccctgtttgctttggagatttggaatacatttttgttgtc-catttccgcatgctgttttgacatacaatctcttcccattt---cagAATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAG

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
gttttgtttcctgtgg-aaagtcttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG
 |  |  |   |||   ||  |||  |   |  |||| | |  |   |||       | |  |||||   || || |  ||  ||  |  | | | |  ||| || || |||||  | |||||||||||||||||||| ||  |||| ||||||||||| || || ||  |||| || || |||||  | |||||||||
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctg-tgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG

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|351017097|gb|FQ424524.1|FQ424524
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|33408128|gb|CF213755.1|CF213755
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|349824324|gb|FQ417683.1|FQ417683
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|33408558|gb|CF214185.1|CF214185
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110390655|gb|EC955577.1|EC955577
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|71876275|gb|DT025330.1|DT025330
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|71866199|gb|DT015254.1|DT015254
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110709953|gb|EE085862.1|EE085862
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|351028488|gb|FQ444769.1|FQ444769
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110691734|gb|EE070172.1|EE070172
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|71876274|gb|DT025329.1|DT025329
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110725014|gb|EE101356.1|EE101356
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|294966596|gb|GW837731.1|GW837731
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110709110|gb|EE084283.1|EE084283
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|71869605|gb|DT018660.1|DT018660
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|351018531|gb|FQ424638.1|FQ424638
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|351028310|gb|FQ427206.1|FQ427206
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
EST: gi|110371348|gb|EC935304.1|EC935304
EST:     AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAG                         AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA
genomic: AGTTGCCAAAAGGACTCCTCCCTCTCAACGCCAATCCGTCCAACACGAAGgttccttctc ... ttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG
                                            cttttat  CT-rich tract
          ttttcttttgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtttcctgtggaaagtcttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG

- - - -ttcctgt
- - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggc