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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA

Basic information

species Vitis vinifera
transcript Vv10s0003g01700.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 1
---cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
   |      ||    |    | |   |   ||| | |   |  |      | | |||||  |  |  | |   | || ||||   |  ||  |     | ||||||||| | ||||||||| |||||||||||| |||||||  || | || ||||||||||||||||||||||||||||| || || |||||  | |||||
tctcgagtgtcactccgtcactcacattcctccgccaaacaaaattccc--tatgtttgatttccatcatttcat-cgattgattgtaactgtttattttcagGGATTTCTCGCAAGACTCAAGAGCTCTACGCGATTGTGTTCGTGGCACGCTATTTGGATCTGTTCACGGACTTCATCTCCGTTTACAACACCTTCATGAA

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------cagcaaccaaagggagcattagggtttcccgtcgagtca---tttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
                                                                  |      ||    |    | |   |   ||| | |   |   || ||| | ||  |||  |       || ||  | |||||  | | |    |     | ||||||||| | ||||||||| ||||| |||||| |||||||  || | || |||||||||||||||||||||||||| || || || |||||  | |||||
gtctctctctcgcggttcccccaaaattggggctattttttattctatttttcaaatgttcattctcgagtgtcactccgtcactcacattcctccgccaaacaaaatttcctatgtttgatttccatcattttaccga--ttgtttggaactgttatttt----tcagGGATTTCTCGCAAGACTCAAGAGCTGTACGCGATTGTGTTCGTGGCACGCTATTTGGATCTGTTCACGGACTTCATATCCGTTTACAACACCTTCATGAA

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G29330.1 (Arabidopsis thaliana), 3'ss of exon 1
-cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
 |  || |  || |||  ||    ||      ||  |   ||   |  | || |         || | ||     |||     ||   |  |    | |||| || || ||||||||||| |||||||| |||||||||||  |||||||||| ||||||||||| ||||| |   | ||  | || ||||   | |||||
gctaca-cggaatggaaaatgcttgtagatgctcatgattttctcatagattgtgcagctcctaacattgttgctgttgacttttggattttgttggctagGAATCTCTCTCAAGACTCAAGAGCTCTATGCGCTTGTGTTCTTGACTCGGTACTTGGATCTGTTTACGGATTATGTATCTCTGTACAACAGCATCATGAA

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ37620 (Selaginella moellendorffii), 3'ss of exon 1
cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
                                           || ||| |        | ||| |     ||| | | | |  ||||      |   |||||| ||||||||||| ||||||||||||||||| || ||  || | || ||  | ||| ||||||| |||||  ||||  |||| |||   || |||||
------------------------------------------gtatggtatggcatcgatcaaagaggcgattcttctcaaaacttcta----aacgcagGGATCTCGCTCAAGACGCAGGAGCTCTACGCGCTGGTTTTCGTGGCGCGCTACCTCGATTTGTTCACAGACTTTGTCTCGCTCTACAACTTCGTCATGAA

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ15071 (Selaginella moellendorffii), 3'ss of exon 1
cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
                                           || ||| |        | ||| |     ||| | | | |  ||    |   |   |||||| ||||||||||| ||||||||||||||||| || ||  || | || ||  | ||| ||||||| |||||  ||||  |||| |||   || |||||
------------------------------------------gtatggtatggcatcgatcaaagaggcgattcttctcaaaactt----taaaacgcagGGATCTCGCTCAAGACGCAGGAGCTCTACGCGCTGGTTTTCGTGGCGCGCTACCTCGATTTGTTCACAGACTTTGTCTCGCTCTACAACTTCGTCATGAA

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|352787179|gb|FQ477799.1|FQ477799
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|110720994|gb|EE097488.1|EE097488
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|110686747|gb|EE064739.1|EE064739
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|110703644|gb|EE080669.1|EE080669
EST:     ATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: ATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|110688848|gb|EE067872.1|EE067872
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|110687293|gb|EE064579.1|EE064579
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
EST: gi|351040756|gb|FQ438300.1|FQ438300
EST:     GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAG                         GGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT
genomic: GAGTATTCTGGTTCTTCTTCTCAAAATTTACGCCACCAAATCTTGTTCAGgtaacactcc ... tccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA
                             gtttgac  putative branch site (score: 4)
                                   cattttctcctcc  CT-rich tract
              tgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcaaccaaagggagcattagggtttcccgtcgagtcatttctagggtttctttgaagtgaaaaactgagttcgtttgacattttctcctccgagttagGGATTTCGCTCAAGACTCAGGAGCTCTACGCGCTTGTGTTTCTGACTCGGTATTTGGATCTGTTCACGGACTTCATCTCAGTCTATAACACTGTGATGAA

- -caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaa