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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagattcccagttcaagtagatgctgaagcctaccagtatttaggttcagaacctgtaaatctagatctttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 5
--taagattcccagttcaagtagatgctgaagccta--ccagtatttaggttcagaacctgtaaatctagatctttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
  | |  ||  |   |   | |  |  | | ||| |  | |  | | |      |    | ||  | |   | || |||| ||  |  || | |  ||||  |||| |||||||||| |||||||| ||||| |||||||||||||| || |||||| |||| |||||||||||||| ||| ||||||||||| |||| |||||
acttaattttacttcttttgaacctctttaggcccagtctatcaatcaaacattgcttttatagtttt---tattgatgattgtatctat-taacattttgtagCTGATCTTGGTGGGTGGACACGTATTGTTGTTGAGAAGCCTTTTGGTAAGGATCTGGAATCTGCAGAGCAACTCAGTACCCAGATTGGACAGTTGTTTGA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 5
taagattcccagttcaagtagatgctgaagcctaccagtatttaggttcagaacctgtaa-atctagatctttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
|    ||  || ||    |      | | |  | |   |  |||     | | |  |||     |  ||   ||||| ||| |     |  | || |  |||| |||||||||||||||||||  |||| || ||||||||||| || |||||| | || ||||||||| |||| ||| |  |||||||| |||| |||||
ttgtctttacattttcttttacattttatggttcctgtttattatccagaaatctagtactgattgtattgatatgactgcatctgcttccttttctt-agCTGATCTTGGTGGATGGACACGTGTTGTTGTCGAGAAGCCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 5
-taagattcccagttcaagtagatgctgaagcctaccagtatttaggttcagaacctgtaaatctagatctttatgaatgccttgatgtgatc---ttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
 |    || |   |||   || ||  ||  |        ||||    | |||||    |||  ||   | |      ||| ||  || || |    |||   |||| |||||||||||||||||||  |||| |||||||| ||||| || |||||| | || ||||||||| |||| ||| |  |||||||| |||| |||||
ttgtctttactttttcttttacattttgtggttcctttttatt---atccagaaatc-taatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------taagattcccagttcaagtagatgctgaagcctac--cagtatttaggtt-------cagaacctgtaaatctagatctttatgaatgccttgatgtg--atcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
                                                           || ||  |  | ||||  ||   | |       |    |||| |||| ||       ||     |  |    | ||  || ||| |  |  |  |||   ||  ||||||||| ||||||||||||||||||| ||||| || |||||||| || ||||||||  | || |||||||||||||| ||| | ||||||||||||||||||||
gtgagtccctttcagctgtggaatttattacttggataaaatgttaacctgcttgagcctaggacacgtatttcatctacgagttagtcttcattttagtagttagcttagaaatacaagttttagacgctttgaagttcatgtaaactatattgtctcataatttccagCTGATCTTGGTGGATGGACACGGATTGTTGTGGAGAAGCCATTTGGCAAGGACCTTGAATCTGCAGAGCAACTGAGTTCTCAGATTGGAGAGTTATTTGA

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
taagattcccagttcaagtagatgctgaagcctaccagtat--ttaggttcagaacctgtaaatctagatct-ttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
             | |  |   || |  |   |   |  ||  |||| |  ||||  | |     ||  |   ||   ||||  |       ||  ||||||||| ||||||||||||||||  | ||||| |||||||| || || || ||||||||||| ||||||||||| || ||| | ||||||||||  || |||||
------------gtgagtttactgttagattttgttaacattattagatagagaatatttggtaataacttcattggaaatgtat-------attgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA

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|30128455|gb|CB913794.1|CB913794
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGNCA-G
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGG-CAAG
EST: gi|30299156|gb|CB975950.1|CB975950
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTTGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|110686452|gb|EE064108.1|EE064108
EST:     AATATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|161717585|gb|FC065623.1|FC065623
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTTGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTTGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|30128024|gb|CB913363.1|CB913363
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|161719304|gb|FC068268.1|FC068268
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTTGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAAT                         CTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTTGGCAAGG
genomic: AGTATATCCGTCTGTCTGCAGGATGATCAAGCTTTGTTGCATGAATAAATgtaagtttcc ... tcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagaacctgtaaatctagatctttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA
                                  ccttgat  putative branch site (score: 5)
                                             tcttttcc  putative PPT
                        tttatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagattcccagttcaagtagatgctgaagcctaccagtatttaggttcagaacctgtaaatctagatctttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - attccca
- - - - - - -tcaagta
- - - - - - - - - - gatgctg
- - - - - - - - - - - - - - - cctacca
- - - - - - - - - - - - - - - - - - - - - - - - cagaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg