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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 3
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
                       | |  | || | |   |  ||| | ||| ||| |||||     | || ||   | | |  | ||||| |  || ||  ||| |   || | | ||||| || || ||||||||||||||||||||  | ||||||||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||| |
----------------------gtatgctccttagtgctagactgctagtg-cttgaagta-----catgattc-cagtgtagtaaatttttacatgtggcaatat---ttatgttcagGACAAGATCTTGCAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAA

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
--------------gtaaacttctcttctcatctccctttattgctgaattagaagctgtt-tgtgtctttaagtattagccttggtttgtaatttgattaatttgtc------tatttg--ttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
               ||||     ||  |  ||| | ||||||    || ||  | |  |  | |    | || | |||  ||    |  | |  ||   |||||||       ||   |  ||  | |||  | |   ||||| || ||  | |||||||| ||||| || |||||||| ||||||||||||||||||||||| ||  | ||||| |||||||| ||||||||||||||||
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatct--actcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 11
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
         |     || |   |  | |   ||||| | | || |||| |  ||     || |     | ||| | ||||||   |   ||||  ||| ||  || || |     | |||| || ||  |||||||||| |||||||| || | ||||||||||||||||||||| |||||||| || ||||| ||||| |||||||| || ||||| |
---------tgggagcaccatgcactttacatgaatgata-gcagtttttccctcgttatagtttttcttgtt-gaaatttgcaaa---tgtcattttttttttgcgtat-----gtagGACAAGATCCTGCAATCAACTGGCAGAGGACGTAATGTTACTGTTACAAATGATGGGGCTACCATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAA

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 2
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagc-----cttggtttgtaatttgattaat-ttgtctatttgttaat-gtgtcttctc-----tgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
       | | || |     |   || ||  ||  || ||| |      | |   | | |  ||||      ||  ||   | | |  ||| | |||   |||||  | | |  | || |      || |||| || ||  |||||||||| || ||||| || | ||||||||||||||||||||| |||||||| || ||||| ||||| |||||||| || ||||| |
------gtatgtttttgaaacatattgttcatgccttggaaccgtccactttacatgaatgatagcagttttttacttctcattgttgttattgttgaaaatttgcaagttgcatttttttgtgtatgtagGACAAGATCCTGCAATCAACTGGTAGAGGGCGTAATGTTACTGTTACAAATGATGGGGCTACCATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAA

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 4
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatt-tgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
              | |  || |||  |  || | |      |||| ||||    | |  | |    ||  ||| || |  | | |||||  | ||| | |  |||||   |  |||||||||||||||||||| |||||||| ||||| ||    |||||||| || |||||||||||||| ||||| |||||||| |||||||| |||||||||||||
-------------gtaaaatctcttcttcactcatt-----actgtatgtggtggtgataaatgattttattttctactcataactaattcatatatct-tggatgtga--taactgcagGATAAAATTTTGCAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACTAATGATGGTGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTA

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 4
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
||||| |   ||  ||| |||  | ||| |  |   ||  |  || || | | ||  | |  || |         ||||||   ||  |||   ||||| |||          |||||||||||||||||||| |||||||| ||||| ||    |||||||| || |||||||| ||||| ||||| |||||||| |||||||| |||||||||||||
gtaaaatctcctcttca-ctcattatat-gtggtggtaataaatgattttattttctactcataac---------taatttatatatcttgg--atttgataa----------ctgcagGATAAAATTTTGCAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACGAATGATGGCGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTA

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|352769329|gb|FQ471478.1|FQ471478
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|71880141|gb|DT029196.1|DT029196
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352782455|gb|FQ470358.1|FQ470358
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|161714038|gb|FC064113.1|FC064113
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352765070|gb|FQ473718.1|FQ473718
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352773730|gb|FQ472512.1|FQ472512
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352777695|gb|FQ466748.1|FQ466748
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352781730|gb|FQ469028.1|FQ469028
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
EST: gi|352777783|gb|FQ466836.1|FQ466836
EST:     CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATG                         GATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT
genomic: CAATGGCGATTGCTGACCTGGTTAAGACAACCTTAGGGCCAAAGGGAATGgtaaacttct ... ttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA
                                 tgttaat  putative branch site (score: 3)
                                         tgtcttctct  CT-rich tract
           taatttgattaatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttctcttctcatctccctttattgctgaattagaagctgtttgtgtctttaagtattagccttggtttgtaatttgattaatttgtctatttgttaatgtgtcttctctgcagGATAAAATTTTGCAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT