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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCACCAACGTGGGAAGGGAAGAGAGATACCACCTCTGGTTCGATCCTTCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatccgtttttgcctatctttagataattcatattcttttaatgttttcttctctaacaactgcccttttcttcttttaatatcgtgaactactt...

Basic information

species Vitis vinifera
transcript Vv01s0011g06250.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G01520.2 (Glycine max), 5'ss of exon 2
GAAGCACCAACGTGGGAAGGGAAGAGAGATACCACCTCTGGTTCGATCCTTCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgta---accatccgtttttgcctatctttagataattcatattcttttaatgttttcttctcta----acaactgcccttttc--ttcttttaatatcgtgaactactt
||||||||| | | || || || || |||||   | | ||||| |||||| |||| ||||||||||||||||||||||| ||||  |||  |  |||||||||   |  || |  | |     |     | ||     || |  || | |  ||||| |   ||    | ||||    | |||   | || || ||| |          
GAAGCACCAGCATTGGTAGAGAGGAAAGATATGGCTTATGGTTTGATCCTGCTGAGGATTTCCATCAGTACAGTATTCTTTGGACAGATTCTAAGATCATgtatgtatgatgcaatctatttgaatcccacatgccatatttggttattacattttccttgttatggtaaaactagtttcttcaactgttctattattgc---------

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G27990.1 (Glycine max), 5'ss of exon 3
GAAGCACCAACGTGGGAAGGGAAGAGAGATACCACCTCTGGTTCGATCCTTCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgta---accatccgtttttgcctatctttagataattcatattcttttaatgttttcttctctaacaactgcccttttcttcttttaatatcgtgaactactt-
||||||||| | | || || || || |||||   | | ||||| |||||| |||| ||||||||||||||||||||||| ||||  |||  |  |||||||||   |  || |  | |     |     | ||     || |  || | |  ||||| |   ||     |     |   |||||| | | || |  | || |  
GAAGCACCAGCATTGGTAGAGAGGAAAGATATGGCTTATGGTTTGATCCTGCTGAGGATTTCCATCAGTACAGTATTCTTTGGACAGATTCTAAGATCATgtatgtatgatgcaatctatttgaatcccacatgccatatttggttgttacattttccttgttatgg--taaaactagtttctttaactgtcct--attattgc

upper sequence: Vv01s0011g06250.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G01850.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGCACCAACGTGGGAAGGGAAGAGAGATACCACCTCTGGTTCGATCCTTCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatccgtttt--tgcctatctttagataattcatattcttttaatgttttcttctctaacaactgcccttttcttcttttaatatcgtgaactactt
|||| ||  |    ||||| |||||||||||  | |||||||| |||||| |||||||||| ||||| |||||||| ||||||  ||||  ||  |||||||||  |          | || ||  |    ||||   | ||  |||  |    | |     |      ||  ||  |  | ||| || |    | ||    
GAAGTACTCATTCAGGAAGAGAAGAGAGATATAATCTCTGGTTTGATCCTACTGAAGATTTTCATCAATACAGTATCCTCTGGTCTGATTCTCACATCATgtaagtaaaaaaaaaagtaccaattctctcttaatctttgtttgtttggttcaatttaaaggaggttaggctattgaccccatttgat-ttaaaagcttta-

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|351013756|gb|FQ433908.1|FQ433908
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
EST: gi|161721792|gb|FC070495.1|FC070495
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
EST: gi|161720664|gb|FC069925.1|FC069925
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTAT
EST: gi|161717715|gb|FC065940.1|FC065940
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGT
EST: gi|161712915|gb|FC062388.1|FC062388
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGA
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGA
EST: gi|71854719|gb|DT003774.1|DT003774
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATC
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATC
EST: gi|110396340|gb|EC962024.1|EC962024
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
EST: gi|30132589|gb|CB917928.1|CB917928
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
EST: gi|351013386|gb|FQ425417.1|FQ425417
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
EST: gi|161720549|gb|FC070921.1|FC070921
EST:     TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCAT                         ATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT
genomic: TCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatcc ... tgtgctgcagATTTTACGTGGACAATGTTCCTATCAGAGAGATAAAGAGGACTGAAGCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCACCAACGTGGGAAGGGAAGAGAGATACCACCTCTGGTTCGATCCTTCTGAAGATTTCCATCAGTACAGTATTCTCTGGAGTGATAATCTGATCATgtaaccatccgtttttgcctatctttagataattcatattcttttaatgttttcttctctaacaactgcccttttcttcttttaatatcgtgaactactt

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttttc