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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atataacaagagggtgcaagagatatctacaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
atataacaagagggtgcaagagatatctacaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG
               |  ||  |  |  | |       |  ||||  ||    ||   |  || |  |||||||||      |   ||||     | |||    || ||||||||  | || ||  | |||||||| ||||||||||||||  |||||||  ||||||| ||||||||  | |||||| ||||||   | 
---------------gtgagtaacttgcaaagttgttgaatctccttcaatctta--ttggaaccacattttctaagagagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
atataacaagagggtgcaagagatatct-acaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG
          | | |  || | |||| | |   | |     | | |||     |        || ||||   | |   | |||    | |||||     ||| | || |||||||| ||||| || ||| ||||||||||||||||||||||  |||| ||  |||||||||| || ||||| || ||  |||||||||||
--------gtaagttataacatatattttatgtatactttgctttcaaagctccaccttgtgaatcctaaact-tgggtgttg----tattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
















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|110370776|gb|EC932910.1|EC932910
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|110699529|gb|EE076605.1|EE076605
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGGATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|110416060|gb|EC982014.1|EC982014
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|27584813|gb|CB007508.1|CB007508
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|110365725|gb|EC929133.1|EC929133
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|110708175|gb|EE085416.1|EE085416
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
EST: gi|161713613|gb|FC062533.1|FC062533
EST:     GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACC                         ATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA
genomic: GGATTATTGACTCTTGCTCCTTATCATTCCGATCGGTTCTTATTGTCACCgtaagttctt ... ttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG
                         ttctaaa  putative branch site (score: 2)
                                tcttgcttctcttttg  CT-rich tract
                     tattttctaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atataacaagagggtgcaagagatatctacaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTG

- - aacaaga
- - - - - - -gtgcaag
- - - - - - - - - - - - - - acaaaca
- - - - - - - - - - - - - - - - - - ccatcct
- - - - - - - - - - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctcaa