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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttcttgctattatgcattaaatgttatgaaagacctctgctttctgatgtatcttgaacctagatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g08600.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G05180.1 (Glycine max), 3'ss of exon 3
gtatcttcttgctattatgcat-taaatgttatgaaagacctctgcttt-ctgatgtatcttgaacctagatgt-tttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
||| | || |  ||  |   |  |   ||||| || | |||  |  |||  ||||  |   |||      |     | |||||||||||| || ||||||||||| |||||||| |||||  |||||||||||||||||||||||||  | |||
gtaccatcatcttaacacataaatctttgttacgagaaacccattttttattgataaagtatgagttataacacactcatgtttgcagGTAAGGAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGATGCGAAAAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G10180.1 (Glycine max), 3'ss of exon 2
-----gtatcttcttgctattatgcatta----aatgttatgaaagacctctgctttctgatgtatcttgaacctagatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
      |  ||   |   | |||   |||    || ||||  |||  ||| |  ||| |  | | |||  |   || |  |||| || |||||||| |||||||||||||| |||||||| |||||  ||||||||||||||||||||||||| || |||
gtaccatccctatctcaaaatatttgttatgataaagttagaaaatccctttttttttttgtatgtct-aatgatacaacttttttgcttgcagGTGAGAAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGATGCAACAAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G05090.1 (Glycine max), 3'ss of exon 4
gtatcttcttgctattatgcattaaatgttatgaa-agacctctgctttctgatg-tatcttgaaccta-gatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
||| |      || | |  ||||||   |||| |  |||   | ||||| |  || ||  ||  |  ||  |   ||| ||||||||||| || ||||||||||| |||||||| |||||  | |||||||||||||||||||||||  |||||
gtaaccatcatct-taacacattaatgtttattactagaaacccgctttttattgataaattagagttataacactttttgtttgcagGTGAGGAGAGAAAAGATTAGTGAGCGAATGAGGTTACTTCAAGAACTTGTTCCAGGATGCGATAAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA0041S00210.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gtatcttcttgctattatgcattaaatgttatgaaagacctctgctttctgatgtatcttgaacctagatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
                                                               | ||  |  | ||||    || | |   |  ||||  ||| |  ||| || ||||| |  ||         ||| || | |||||| |||||||||||||| |||||||| |||||  |||||||||||||||||||||| || || |||
gtgagagctagaagaggtcaagccactaacagccacagccttgcagaaagagtaccatccctatctcaccacgatatttgctatgagaaagttagaaaacccttt--tttttgttgtatgtctaatgatacaactttttgctcgcagGTGAGAAGAGAAAAGATTAGTGAGCGAATGAGGTTGCTTCAAGAACTTGTTCCAGGTTGCAACAAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA0041S00210.1 (Glycine max), 3'ss of exon 5
------gtatctt-cttgctattatgcattaaatgttatgaaagacc---tctgctttctgatgtatcttgaacctagatgt-----tttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGG----ATGTAATAAG------------------------------
      ||| ||  | | | |  |||  |   ||||||||| | |||   | |   || | || | | |     || | | |     ||| || ||| |||| || ||||||||||| |||||||  |||||  |||||||||||||||||   |     || | || ||                              
tgcacggtacctaacataccacaatgtttgttatgttatgagaaaccaattttttatttttatttttgtaatgtctcgttatacaactttttgcttgtagGTGAGTAGAGAAAAGATTAGTGAGCAAATGAGGTTGCTTCAAGAACTTGTTTTGGTTTACATATCATCAGTAACGGACCCAGTACTGAAACTTATCAAAG

upper sequence: Vv18s0001g08600.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G10120.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gtatcttcttgctat-tatgcatta----aatgttatgaaagacctctgctttctgatg-tatcttgaacctagatgttttat------gtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
     |  |||| |  || | |||  ||||    ||| |  |    |   |||||    |  || |     |||  | | | |||  |       |||| |||| ||||||||||||||||||||  | |||||| ||||||||||||||||||| ||||| || |||
gtaaggactcttttacctgtatatagattatgagaatctgctctttgttttctgccaattactggtgctgagaagtttgctatttcttttgttgttttgaagGTTAGAAGAGAAAAGATCAGTGAAAGGATGAGATTGCTTCAAGAACTTGTTCCCGGATGCAACAAG

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|161708702|gb|FC059231.1|FC059231
EST:     TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGG                         GTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT
genomic: TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGGgtatcttctt ... atgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT
EST: gi|349819168|gb|FQ412062.1|FQ412062
EST:     TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGG                         GTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT
genomic: TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGGgtatcttctt ... atgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT
EST: gi|351053379|gb|FQ455715.1|FQ455715
EST:     TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGG                         GTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT
genomic: TGAGGGCCAGAAGGGGCCAGGCGACTAATAGTCACAGCCTTGCTGAAAGGgtatcttctt ... atgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaagacctctgctttctgatgtatcttgaacctagatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG
                ttctgat  putative branch site (score: 3)
                                         ttttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttcttgctattatgcattaaatgttatgaaagacctctgctttctgatgtatcttgaacctagatgttttatgtttgcagGTCAGAAGAGAAAAGATCAGTGAGCGTATGAGACTGCTTCAAGAACTTGTTCCAGGATGTAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG