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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacttgtgtgtgcacatgcttgcatctttttatacttattacagtatttgtacagaagtaaccatttttaatgttttggctaatgtcactgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCCGGGGAACGCTTTTGACATCAAATATCTCGTCCCAGGTTGTCTAAGAAGT

Basic information

species Vitis vinifera
transcript Vv04s0008g03170.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA04G07850.2 (Glycine max), 3'ss of exon 14
-------------------------------------------ctacttgtgtgtgcacatgcttgcatctttttatacttattacagtatttgtacagaagtaaccatttttaatgttttggctaatgtcactgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCCGGGGAACGCTTTTGACATCAAATATCTCGTCCCAGGTTGTCTAAGAAGT
                                           |   || |||     ||      | | ||| | | ||||     | | || || | |  |||   |    || |  ||     || |   | || | |||||||||| | |||  ||||||||||  |||| ||  | |||||||||||||||||||| ||| | ||| ||||| | || ||||||||||| |||||| |
gtaagctatttgatagttcaatagtggcaatgtggtttgccatcctattatgttattgcaaataatcttttttatcttcttaaagtggaaattttagatacataaaagtcagaaaagaatt-----atattcatctttcgcagATGAGCTTTGTGATGATAAAATGGATCTGCAGCATACCGAGGAAGGGTTCCGGGGAACACTTCTCACAGCAAATGTTTCATCCCAGGTTGTTTAAGAACT
















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|33408006|gb|CF213633.1|CF213633
EST:     TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAG                         ATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC
genomic: TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAGgtaagttatt ... tgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC
EST: gi|30135690|gb|CB921028.1|CB921028
EST:     TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCNGGATATTGCAG                         ATGAGCTCTCTGACCATAA
genomic: TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAGgtaagttatt ... tgttccacagATGAGCTCTCTGACCATAA
EST: gi|110396979|gb|EC962688.1|EC962688
EST:     TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAG                         ATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC
genomic: TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAGgtaagttatt ... tgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC
EST: gi|33407921|gb|CF213548.1|CF213548
EST:     TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAG                         ATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC
genomic: TCTTCTTTGGGTGAAAGATTCAGAGATCCATGAGTATCGGGATATTGCAGgtaagttatt ... tgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtacagaagtaaccatttttaatgttttggctaatgtcactgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCCGGGGAACGCTTTTGACATCAAATATCTCGTCCCAGGTTGTCTAAGAAGT
                                            ctgttcc  CT-rich tract
                   atttttaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacttgtgtgtgcacatgcttgcatctttttatacttattacagtatttgtacagaagtaaccatttttaatgttttggctaatgtcactgttccacagATGAGCTCTCTGACCATAAAATGGAGGTGCAACAGGCTGAGGAAGGGTTCCGGGGAACGCTTTTGACATCAAATATCTCGTCCCAGGTTGTCTAAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - gtgtgtg
- - - - - - -cacatgc
- - - - - - - - - - -tgcatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - agaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg