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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT

Basic information

species Vitis vinifera
transcript Vv11s0206g00130.t01
intron # 5
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 5
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 5
agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggc-ctgaatgttgtttgc-taataccaaaagctgacggtggtggttgaaac-agATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT
      |  |  | |  || | |||     |   |||  || | | ||    | |  |||     |  |  |    |  | |   | |  |  ||    | ||||||||||||||||||| |||||||| || || ||||||| |||| | | |  |||  |       |   |  ||   | | | | |             
---ggaccctttttaacttacattttttgtttgttaagttttatcttgattaccgtttgtctccagaattttgttgagggatattgtttttcttttcttccagATGTTCTACAAGCAGGCAAAGAAAACAAACCAATGCTGTACTATACTCTGAAGTTTGGACTTTCCTGT--CCTTAAGATGAAGACTCCAG----------

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 5
agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggc-ctgaatgttgtttgc-taataccaaaagctgacggtggtggttgaaac-agATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT---
      |  |  | |  || | |||     |   |||  || | | ||    | |  |||     |  |  |    |  | |   | |  |  ||    | ||||||||||||||||||| |||||||| || || ||||||| |||| | | |  |||  |   |     ||  ||   |     | |  ||  | |  | |   
---ggaccctttttaacttacattttttgtttgttaagttttatcttgattaccgtttgtctccagaattttgttgagggatattgtttttcttttcttccagATGTTCTACAAGCAGGCAAAGAAAACAAACCAATGCTGTACTATACTCTGAAGTTTGGA---CTTTCCTGTCCTTAAGATGAAGACTCCAGGTTAATTTTGCT

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 3'ss of exon 5
-agatagcagtagtaaggttccttt--tagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCC-TCACATCA-CGTGT-
  ||       | | ||     | |  ||  | | |||    |||| |    |  | | |  || |   |  | |  |    || |  |  | ||| |  |||||||||||||||||||| |||||||||||    || ||||  ||  |||||   |  |||  |     |    | ||| | | || |   |  |   | | | 
atgaccctttcattcagtgctatctgataatattttctgttgttaatcaatcggttcagttatgatcttttgtgctgat--ttgtccctccttgtt-atgcagATGTTCTACAAGCAGGCCAAGAAAACCAACTCTTGTTGTACAATCCTGTAA---TAGAAACTCTGGTATAGAGTTCTGCAGTAGCACACTATGTTGGCATTTT

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 5
---agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagct-gacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGC---TTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT
      |  | | ||  |  || || |||   ||   |  | ||     ||  |   | |    ||| || | || | || || || | ||| | |||||||||||||||||||| ||||| ||||||||||||||||| ||||  |||||||||||    ||  ||       ||   |  | ||  | | | | | |||  ||  
ttgctttttcggaagagaactttctgttaaccattaatggaattttatttgcccactagt----tttactgacacaagaatcttgatgctggcgtttgaaacagATGTTCTACAAACAGGCCAAGAAAACCAATCAGTGTTGTACCATATTGTAAGCAAGCTTTCAAGCTGTCAGTATGCAGC-GTGCTCGTCTTGA-ATCCTGTT-

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 6
-----agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTA-ATGGCCCTCACATCA--CGTGT-
     | |    | | |   ||||   |  |  |     |    |||| | |      |||| || |||| | |      ||  ||| | ||| | |||||||||||||||||||| ||||| ||||||||||||||||| ||||  |||||||||    ||||      | ||  |  | | |  |  |  ||||| | |  | ||| 
ttgatacaccatatttggctggttttctggaagatcactttctgttaaccattaatg-gaattttatttgttcact----aacttgatgctggcgtttgaaacagATGTTCTACAAACAGGCCAAGAAAACCAATCAGTGTTGTACCATATTGTAA----TCAAGCTTCCAAGTCTTTCATTATGCAGCGTGCTCACTTGAATCCTGTT

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaa-----gctgacggtggtggttg----aaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCA---AAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT
                 ||  | |    |   |   || ||     ||| |   |||  |  |          |  || || | |  | ||     | |     ||||| |||    ||||||||||| |||||||| ||||||||||| ||    || ||||   |  | |||||| | |   ||  |     ||  |  || ||         ||   ||    
gtaacattccaccctagtattacttactactgtttcttcagtggattctgagggtaatgggagatagatgaaatagtttctgacatgagaatattggtttgttttggtgtttggatgaaacagATGTTTTACAAGCAAGCGAAGAAAACAAACTCATGTTGTACACTTCTCTAAGCTGTAATGCAACTCTTGAATGTCCCTCTATAGAATAGTCTACCCTACT---

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 6
agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacg-----gtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT
       |       |  ||     | |    ||   | |||     ||      |||||   | | || |  |||| ||||       ||  |||||| |||||||||| |||||||| ||||||||||| |||   ||||||| |||  ||| ||||   |        ||   | || |  |     | |    |   | | 
-----atatcctctggaatctcaagatattcttcgttatttagattaggtaaaccatgtttacttccaacatgaaaatctgatttggttgtattggttggaacagATGTTTTACAAGCAAGCGAAGAAAACAAATTCATGCTGTACTATTCTGTGAGCTGGAAGTCCTGCTGGGTATATAGTCAACCAAACTTTTGCTGGGGGGA

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ35352 (Selaginella moellendorffii), 3'ss of exon 5
agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT--------
                                             ||   |   |    | ||| | |       || ||  | |      |||   |||||||| |||||||| || ||||||||||| |||||||| || || |||| ||        ||| | |    | |  |  ||    |   ||||  |||||        
---------------------------------------------gtattcaaaatctctcttttcaatcgtatcaaactcccagc-----ttg---cagATGTTTTACAAGCAAGCCAAGAAAACCAACCAGTGCTGCAGCATCTTGTGAG--------AGCGACGCGATTTTGATAAAACTCGCTATACATACCGTGTGTTGATGT

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:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|33408128|gb|CF213755.1|CF213755
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|349824324|gb|FQ417683.1|FQ417683
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|71881424|gb|DT030479.1|DT030479
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|33408558|gb|CF214185.1|CF214185
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|110390655|gb|EC955577.1|EC955577
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|71876275|gb|DT025330.1|DT025330
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|71866199|gb|DT015254.1|DT015254
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAAC-AATCAGTGCTGTAGTATATTG
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTG
EST: gi|110709953|gb|EE085862.1|EE085862
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|351028488|gb|FQ444769.1|FQ444769
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAANACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|110691734|gb|EE070172.1|EE070172
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|110725014|gb|EE101356.1|EE101356
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|30125802|gb|CB911141.1|CB911141
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|294966596|gb|GW837731.1|GW837731
EST:     AGCTGGACGGTTTAGTTGAGAAAAGTTCAGATCTCACCACAGCATCCCAG                         ATGTTCTACAAGCCGGCG
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCG
EST: gi|110709110|gb|EE084283.1|EE084283
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTAAATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|71869605|gb|DT018660.1|DT018660
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|351018531|gb|FQ424638.1|FQ424638
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|351028310|gb|FQ427206.1|FQ427206
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
EST: gi|110371348|gb|EC935304.1|EC935304
EST:     AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG                         ATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA
genomic: AGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAGgtacctgtac ... gttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT
                     taata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatagcagtagtaaggttccttttagaaatctctaaacttaagcgtgggcctgaatgttgtttgctaataccaaaagctgacggtggtggttgaaacagATGTTCTACAAGCAGGCGAAGAAAACCAATCAGTGCTGTAGTATATTGTAAGCTTTCAAAAGCAAAGGTGCTCTACTGTAATGGCCCTCACATCACGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - -agaaatc
- - - - - - - - - - - - - - - - - - - - - - - - ggcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg