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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtcatcttattgttaagtatcttgcatttccagcattgctaaggggcatatcaggatcttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG

Basic information

species Vitis vinifera
transcript Vv04s0023g02970.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 2
gtgtcatcttattgttaagtatcttgcatttccagcattgctaaggggcatatcaggatcttgctactgaaacatc-tcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG
                  || | |   |      |||    |  |  | ||  ||  || ||  |||   | |  | |   || |        ||   ||||||||  | ||||||||  | |||||||||||||| || ||||| ||||| || || |||||||||||||| |||
------------------gtttgtgagacgaggtgcacgcgtttgttggatgccaaaatattcttacctgatcggcgttgttggttctgtggctt---cagGAGCCTCTCAAGCTGGACTTTGTCATTAGCTTTCCGGACCATGGATTTCACCTACGCTTTGATCCTTGGTCCCAG

upper sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G37380.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gtgtcatctt--attgttaagtatct-tgcatttccagca--ttgcta--aggggcatatcaggatcttgctact---gaaacatctcactgatatgacaattt----atacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG
                                                        |||| | |||  |    ||| |  || |    |||  |||  || |||  |   |    |  |  | ||  |  |   || |    | |||  |   ||  | |    || ||||| ||  | ||| ||||||| || ||||||||||| |||||||| || ||||||||||| ||||| ||||| |||
gtttgtcacatatgattatcacttaacaccttgtcagttgtgtcgtctatgattttgtgtgaacttgaacgagtaattgactgtctgcttcacgcaggttactactatctgtggctttgcgttttattttttaagagattcttgacttcttctactttatgcacatgcagGAACCCCTGAAGTTGGATATTGTTATTAGCTTTCCTGATCATGGATTCCATCTTCGTTTCGATCCGTGGTCTCAG

upper sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------gtgtcatcttattgttaagtatcttgcatttccagcattgctaaggggcatatcaggatcttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG
                                                                                                            |||    ||    ||  |   ||    ||       ||  | |  |    ||  |  | ||  |  |||    |   ||| | |||       || ||||| ||  | ||| ||||| | || ||||||||||| |||||||| || |||||||| |||||||| ||||| |||
gtttgtcgcatatgatttatggcttaacttactgtcatttatgttttctattattgtttgaacttgcactagcaattgactgtctgcttcgggcaggttactactatctgttgctttgcctttgtgaggctcctgttgttttattttttgaaagatgcatttg--tttttatcttgagttcttctactta-atg----cacatgcagGAACCCCTGAAGTTGGATGTTGTTATTAGCTTTCCTGATCATGGCTTCCATCTTCGCTTTGATCCGTGGTCTCAG

upper sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtcatcttattgttaagt-atcttgcatttccagcattgctaaggggcatatcaggatc-ttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG
        ||  |  || || |       | |     | | ||      ||  | |   || ||| |  |  |   |   |    |  |     | || ||||| || || || |||||| | || |||||||||||||||||||| ||||||||||| |||||||| ||||| |||
-------gtttgtactaggtcacggattgtattagatacttcttttatccaacttatcttcattgtttgttgagttttctatgattccgttgcctcatgcagGATCCTTTGAAACTGGATGTTGTTATTAGCTTTCCAGATCATGGGTTTCATCTTCGATTTGATCCCTGGTCTCAG

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|161713938|gb|FC062598.1|FC062598
EST:     AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
EST: gi|30133248|gb|CB918587.1|CB918587
EST:     ACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: ACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
EST: gi|110718343|gb|EE095064.1|EE095064
EST:     AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAGGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
EST: gi|294963767|gb|GW836617.1|GW836617
EST:     AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
EST: gi|110730101|gb|EE106793.1|EE106793
EST:     AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
EST: gi|27586273|gb|CB008968.1|CB008968
EST:     AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAG                         GAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT
genomic: AGCAACAGCCTAACATTTACGATGTTGTCCACGTCAAGTATTTTGACGAGgtatgcacca ... atttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggcatatcaggatcttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG
                                cactgat  putative branch site (score: 3)
                                     atatgacaatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcatcttattgttaagtatcttgcatttccagcattgctaaggggcatatcaggatcttgctactgaaacatctcactgatatgacaatttatacagGAGCCATTAAAGCTGGATATAGTCATTAGCTTTCCAGATCATGGTTTTCATCTTCGTTTTGATCCTTGGTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - cagcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg