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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT

Basic information

species Vitis vinifera
transcript Vv12s0035g02180.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 3'ss of exon 3
tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaa-aaactcat--ggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
   |   ||  ||   |  |  | | ||  |   |    | ||   || ||||  ||    |   |  |||| |  | |  |||||| | | |  |||   |||| ||  | ||||| || ||  | ||||| || ||||| |||||||||||||| || || |||||||| ||||||||||| ||||| ||||||||||| |
ggagggagtacatagcagtagctagtaaaaaaaatccagatgaacaaataaacggatttaacatatcaattggtact-tattttatggtctgtcatta--cagGTTCTTTTGAGCCGGTTAAGGCTCTTCTTAAGTCCTGGTTATCCATATGAAGAGATCCTCAGGACATTCCACAATCAAACAAGCATTATTATGTGCTCTT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G003379_T01 (Zea mays), 3'ss of exon 3
tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
|  ||  ||   |  ||||||    || | |   ||||          |    |||   ||  | |  |    ||| ||||   || | ||     | |||| || |||||||| |||||  | |||||||| ||||| |||||||||||||| |   |||| ||||| ||||| ||||| ||||| || ||||| || |
tgggccggtctctttaataaatagagagtaacattttgtttaccgttgagtgacatatttgtcttacagtacttattcttttatttgtgttacatttcagGTTCTTCTAAGCCGGTTGAGGCTTTTCTTGAGTCCTGGATATCCATATGAAGAGACCTTGAGTACATTCCACAACCAAACTAGCATTATCATGTGTTCCT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
-tttgcatgttgat-caaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcatt--gctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
  ||  |||||  |   ||||  ||      | |||   |  |  ||   ||  | |  |    | ||||   ||||| || | | |||  | || | | |||||| || || || |||||||| ||||||||||| |||||||||||||||||||||||| ||||||| ||||||||||| || |||||||| |||||||| |
tctttgatgttcctattaatatcatccatgatcttgcaggttatggt---aattttagtgaaaatacatttgactgatttgatctttgtcatcttgt-atttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G00710.1 (Glycine max), 3'ss of exon 1
tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
                        | | |   | |||       | |  |||  ||         |||    |  |   |  | ||||  | ||| |||||| || || || |||||||| |||||| | || ||||| ||||| |||||||||||| | || |||||||||||||| ||| ||||| | |||||||| |
------------------------gtactctctatttcttcactttaccaaca-ataaacaaactattct--acttatctcctcttttcattttatttagGTTCTTCTCAGTCGTTTGAGGTTGTTCCTCAGTCCTGGTTATCCCTATGAAGAAATTTTAAGCACATTTCACAATCAGACCGGCATAGTCATGTGCTCCT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 3
tttgcatgt-tgatcaaataaaattggaattattgtttgcaaga-gtcaaaaactcatggctggttcatt--gctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
  |  | || || | || ||  ||||    |  |  ||||| |   |   ||  | |  |    | ||||   ||||| || ||| |||  | || | | |||||| || || || ||||| || || |||||||| || ||||||||||||||||||||| | | ||| |||||||| || || |||||||| |||||||| |
--tataggtctggttaattatgattgctgctgat-cttgcatgttatggtaattttagtgaaaatacatttgactgatttgatttttgtcatcttgt-atttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G40090.1 (Glycine max), 3'ss of exon 1
tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
                      |  | |   |   ||   | | ||||    | |        ||||| |    |||  || | || | |||| | |||||| || || || |||||||| |||||| |||| ||||| | ||| |||||||| ||||| |  |||||||||||||| ||  ||||| | |||||||| |
---------------------gtacgcaccttcaattctca-attcaatttttaaacttcaagtcatttc----atgtcttgtcttgtcttct-atttagGTTCTTCTCAGTCGTTTGAGGTTGTTCCTGAGTCCTGGTTTTCCCTATGAAGATATTCTAACCACATTTCACAATCAGACAGGCATAGTCATGTGCTCCT

upper sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tttgcatgttgatcaaataaaattggaattattgtttgcaagagtca---aaaactcatggctggttcat--tgctgata--tgctttatgtttttttcttaatt--agGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
           |||    | |   |    ||    || ||   |      |||      | |   || ||    |||  | ||  |   |  |||   |   |||    |||  || ||||  | ||||| ||||| |||||  |||| ||||| |||||||||||||||||||| ||||| || |||||||| ||||||||| | ||||||||||
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT

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|110715902|gb|EE094479.1|EE094479
EST:     CTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: CTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|110371632|gb|EC935746.1|EC935746
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATAT
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATAT
EST: gi|110710843|gb|EE087364.1|EE087364
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGNGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|110703053|gb|EE079560.1|EE079560
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|110716453|gb|EE091450.1|EE091450
EST:     CAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: CAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|33409937|gb|CF215564.1|CF215564
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|110715796|gb|EE094253.1|EE094253
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|30298694|gb|CB975488.1|CB975488
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|33407421|gb|CF213048.1|CF213048
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
EST: gi|37189926|gb|CF609275.1|CF609275
EST:     GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAA                         GTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA
genomic: GCCCAGATTATGGTATACTTAGCTGGGACAACAAGCTTGCTGGTGCTCAAgtaagttagt ... tcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
                      tgctgat  putative branch site (score: 3)
                                ctttatgtttttttct  putative PPT
                           atatgctttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcatgttgatcaaataaaattggaattattgtttgcaagagtcaaaaactcatggctggttcattgctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT

- -gcatgtt
- - - - - - - aaataaa
- - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - -caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - tcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatatgc