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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgtttgacagataactgtcatcttcatctatcatctccaacctttatatttccactaaaaaaatgaattctgacatatcatttccttttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATCGTAATTGCAGCTTAATCAGAAAATTCTTAGAGTCCAATCATAGAGCAGA

Basic information

species Vitis vinifera
transcript Vv02s0012g01850.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 6
atcatgtttgacagataactgtcatcttcatctatcatctccaacctttata---tttccactaaaaaaatgaattctgacatatcatttccttttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATCGTAATTGCAGCTTAATCAGAAAATTCTTAGAGTCCAATCATAGAGCAGA---
||| ||||          |  ||   ||| | | || | |  || ||| ||    ||| | ||   ||  | || | |  | | |   ||  | |   ||||||| |||||||| |||||||||||||||||| | || || || || ||||| ||  |||| ||||| ||| |||| |||     | | || ||  | || |   
atcttgttcttttatc--ccatccatttcttttttccttttaaagcttcatgtatttttctctgttaatctcaaatgtt-cttgtttgtttttatatatgcagACATGCTTGCTTTTGGTGATATTTGGGATCGTGCTTCTAATCGTCATCATTGTTCTTGCTGCTTAGTCA-AAAACTCTCGA--TTCTATTATGAATCAAATGC
















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|349814626|gb|FQ399266.1|FQ399266
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|349814672|gb|FQ400310.1|FQ400310
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATC-TCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|349807660|gb|FQ402051.1|FQ402051
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|110403262|gb|EC964685.1|EC964685
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|349828272|gb|FQ416225.1|FQ416225
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGGA-CAT
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTG-ATCAT
EST: gi|349823620|gb|FQ415030.1|FQ415030
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|349821234|gb|FQ404366.1|FQ404366
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|110369733|gb|EC933900.1|EC933900
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC
EST: gi|349817337|gb|FQ405341.1|FQ405341
EST:     AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTG                         ACCTGCTTGCTGTTGGTGATATTTGGGATC-TCCTCCTCATTGTGATCATC
genomic: AATCCCAACTTGCAAAAGCATCAAAGACCCAACGATCAAATTCATCTCTGgtaatcttga ... tttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatatttccactaaaaaaatgaattctgacatatcatttccttttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATCGTAATTGCAGCTTAATCAGAAAATTCTTAGAGTCCAATCATAGAGCAGA
                          ttctgac  putative branch site (score: 2)
                                  tatcatttccttttct  CT-rich tract
            actaaaaaaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatgtttgacagataactgtcatcttcatctatcatctccaacctttatatttccactaaaaaaatgaattctgacatatcatttccttttcttgcagACCTGCTTGCTGTTGGTGATATTTGGGATCATCCTCCTCATTGTGATCATCGTAATTGCAGCTTAATCAGAAAATTCTTAGAGTCCAATCATAGAGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-tcatgtt
- - - - - acagataa
- - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - - - -catctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - tttccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacat