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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggttgcaagagatcataaatgcttcatgtttttctatcttataaaacttgcaagagatcataaatgtacctctctcacatgtctcttatggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAAGAATAATATGGGCATGCTCTTGGAACCCATTTGGTCATGAATTTGCAAC

Basic information

species Vitis vinifera
transcript Vv01s0011g04130.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os08g38570.1 (Oryza sativa), 3'ss of exon 9
taggttgcaagagatcataaatgcttcatgtttttctatcttataaaacttgcaagag--atcataaatgtacctctc--tcacatgtctcttatggaac-ctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAAGAATAATATGGGCATGCTCTTGGAACCCATTTGGTCATGAATTTGCAAC---
  |   | |     || ||    ||    |||  |  |  ||   |||||  ||| |   |||     ||||  | |   |  |||  | ||| || ||| |||| ||   | | ||     || || ||| | |||| ||  || |||||||||||||| |||||||||||||| |||||||| ||  |  | |||||||||||   
--gtaaggacttcttcctatgatctagtagttcctacaaatttgtaaactgccaatatttatctgttgtgtaattattgatgtcattccacttgtgtaactctagATG---ATGGAGCAGAGCATCATCTTGTTGCAAAGCTTGAAGCACACAAAAGAATTATATGGGCATGCTCATGGAACCCCTTCAGCTACGAATTTGCAACTGG

upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G042371_T01 (Zea mays), 3'ss of exon 6
-------taggttgcaagagatcataaatgcttc-atgtttttctatcttataaaacttg-----caagagatcataaatgtacc---tctctcac-atgtctcttatggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAAGAATAATATGGGCATGCTCTTGGAACCCATTTGGTCATGAATTTGCAAC---
       ||  |   | || |   ||  | |||  |  || ||  ||   ||    |||      || |   |   |  ||| |     ||   |  || || ||| || ||     |   |   | ||     || |  ||  | || | ||  || |||||||||||||| |||||||||||||| |||||||| || ||  |||||||||||||   
gtaggcataattcttatgataatgtagttcctttgaaattatttcataacatttgtcttttcactcatgctgtttcatttgtgctggagctgatatgatatcacttgtgtaattctagAAGGA--GGAGCAGAGCATCGTCTGGTTGCGAAGCTCGAAGCACACAAAAGAATTATATGGGCATGCTCATGGAACCCCTTCGGCTATGAATTTGCAACTGG
















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|34546608|gb|CF514840.1|CF514840
EST:     GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAG                         GTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA
genomic: GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAGgtatgctaaa ... tggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA
EST: gi|34546788|gb|CF515020.1|CF515020
EST:     GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAG                         GTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA
genomic: GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAGgtatgctaaa ... tggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA
EST: gi|37187736|gb|CF607089.1|CF607089
EST:     GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAG                         GTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA
genomic: GTCTGTCTCCAGGGATCGCCAGTTTTCTGTTTTTGCAATAAAAAGAACAGgtatgctaaa ... tggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttgcaagagatcataaatgtacctctctcacatgtctcttatggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAAGAATAATATGGGCATGCTCTTGGAACCCATTTGGTCATGAATTTGCAAC
                            ctctcac  putative branch site (score: 3)
                                      tctcttat  putative PPT
             atcataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggttgcaagagatcataaatgcttcatgtttttctatcttataaaacttgcaagagatcataaatgtacctctctcacatgtctcttatggaacctagGTGTGGACGAAGTCAGTCACCAGCTTATAGCAAGGCAGGAGGCACACAAAAGAATAATATGGGCATGCTCTTGGAACCCATTTGGTCATGAATTTGCAAC

- - - -caagaga
- - - - - - - - - - - -cttcatg
- - - - - - - - - - - - - - - - - - - - - ataaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtc