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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagtaattaccttacctgtcaagaaacaaattcatgttctgggttctcaatgccatccattttccttgctttctaagatatcaatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 8
ccagtaat-taccttacctgtcaagaaacaa-attcatgttctgggttctcaatgc-catccattttccttgctttctaagatat-caatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGA---TGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG
   | ||  | |||| | |    ||       |    |  | ||     |||||||    |  ||||  ||   |  |  | ||| |  |||   ||||   |||||||  | | |||||||| ||||||||| ||||||||||||||   ||| ||| ||||||| || || ||||||||||| |||||
-atgcaacgttccttgcataatgagctttgctagcagttatttgtaagatcaatgcatgacagttttatttatgtcttgtgctattccttttgtgtctt---agTTTGACCCAGTAAAACTAAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G39870.1 (Glycine max), 3'ss of exon 8
ccagtaattaccttacctgtcaagaaacaaattcatgttctgggttctcaatgccatccattttcct---tgctttctaaga-tatcaatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGA---TGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG
  ||   | | || |  |   |    |  | || |  | || | ||   |||    |  |   ||||   |  | | ||| | | |   | | ||| |   |||||||||||||||||  ||||||| ||| ||||||| || || ||   ||||||||| || ||||| || |||||||||||||||||
--agccttcaactgaaatcctatatga--agtttacttgcttgatttgaaatatagtggaaactcctacattttgtttaatactttttgtgttcatgtatccagTTTGATGCTGCAAAGTTAAGGAAGCTTAGACCAAGCTTTAAAGAGGTTGGGGGTTCTGTGACTGCTGGCAATGCTTCTAGCATAAG
















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|30301836|gb|CB978630.1|CB978630
EST:     GTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|77584049|gb|DV221063.1|DV221063
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|30301768|gb|CB978562.1|CB978562
EST:     AGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: AGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|77586184|gb|DV222186.1|DV222186
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|37190107|gb|CF609456.1|CF609456
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCGAGAAACAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|110358833|gb|EC923335.1|EC923335
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|71877133|gb|DT026188.1|DT026188
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGC
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGC
EST: gi|30298600|gb|CB975394.1|CB975394
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|110378421|gb|EC943552.1|EC943552
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAG                         TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT
genomic: GGAGAGGAAAGCCATCTACACTTGTTGATAAGGATGAAGGTCTAGGAAAGgtaaatagaa ... atcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaatgccatccattttccttgctttctaagatatcaatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG
                                        tttccatctt  CT-rich tract
                             taagatatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagtaattaccttacctgtcaagaaacaaattcatgttctgggttctcaatgccatccattttccttgctttctaagatatcaatttccatcttgacagTTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - -cctgtca
- - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - ctcaatg