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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaacctggacctcctcattctcacccctaaactttgctgccggagctgtgctttgggagcattgtagtagaaaaatatgaacacattccttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCTGGTTACCCTCCAGACCCAAATGATCCTGAGTATGATAAGTTAGCTGCCT

Basic information

species Vitis vinifera
transcript Vv07s0130g00170.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G38120.1 (Glycine max), 3'ss of exon 2
----------------gaaacctggacctcctcattc-tcacccctaaactttgctgccggagctgtgctttgggagcattgtagtagaaaaa-----tatgaacacattccttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCTGGTTACCCTCCAGACCCAAATGATCCTGAGTATGATAAGTTAGCTGCCT
                  |  ||    |    ||| | | |    |  || ||| | |  ||     | || |      ||   |||  ||       ||||    |||    | ||| ||| |||||||||| ||||| || || || ||||||||||||||||||| |||||| |   | || ||||||| |||||| || ||  |      ||| || |
gtataactctgactgaagatgctactgcaagccatgcatgatttgtttacattggttcttgaagaaagtttagaagtagttcccgtaataatggactttatgtttgcatattctcttttcagTCTTTGAAGCATAATGGGAGTCTATATGCTCATGTTTTCTTTGCACACTCTGGCTTTTCGCCTGACCCAAGTGATCCAGAATACCAGCCTCAAGCAGCAT
















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|161714627|gb|FC063587.1|FC063587
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
EST: gi|110701765|gb|EE079713.1|EE079713
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
EST: gi|110728716|gb|EE104530.1|EE104530
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
EST: gi|37185372|gb|CF604725.1|CF604725
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
EST: gi|352781182|gb|FQ466495.1|FQ466495
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
EST: gi|352776527|gb|FQ474829.1|FQ474829
EST:     GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAG                         GCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT
genomic: GGGGACCACAGAGTACCAGGTCTCTTTCTTTGAAGTATTATCCATCTGAGgtaccatccc ... ttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtgctttgggagcattgtagtagaaaaatatgaacacattccttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCTGGTTACCCTCCAGACCCAAATGATCCTGAGTATGATAAGTTAGCTGCCT
                                     cacattccttttttcc  CT-rich tract
                    tagtagaaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaacctggacctcctcattctcacccctaaactttgctgccggagctgtgctttgggagcattgtagtagaaaaatatgaacacattccttttttccagGCTTTGAAGCACAATGGTAGCCTCTACGCTCATGTTTTCTTTGCACGCTCTGGTTACCCTCCAGACCCAAATGATCCTGAGTATGATAAGTTAGCTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- -acctgga
- - - - - cctcctc
- - - - - - - - - - ctcaccc
- - - - - - - - - - - - - - - - - - gctgccg
- - - - - - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattcc