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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g04240.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
---------------------------------------gcatgatctctgatcttctc---cctctggacacacaatc---atatgaagtttcgttctc-tcagaat--ttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
                                             | ||||  |||| |     |||| ||   |  |    |||||   ||  | |  |  || ||    |||| | ||  |  |  |    | | | || |  |||  |||||||| || || |||||||||||||| || |||||||||||||| ||||| || || ||||||
gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgc-cagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G470653_T01 (Zea mays), 3'ss of exon 4
gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
   |   |  ||  |      |   |  |  ||| |    | |    ||  |  ||| |  ||     |||         | |  ||  | ||         |||||||| || || |||||||| |||||||| |||||||| || || ||||||||||||||||||
--gtaggcattggacactggacagcg--cgtacagttcactcagcactcagttgctctgtcttaattcaataagctcgtttgatctcccttgtccccg---gcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G481261_T01 (Zea mays), 3'ss of exon 5
gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttca-tcacttctttggttttgatgt--acagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
                     |  |||||||   |      | | |   |||| ||||| | |    |  |   |||| | ||  ||  |     |||       |||||||| || || |||||||| |||||||| |||||||| || || ||||||||||||||||||
----------------gtaggcattggacactggacagcgcgcaat---gttcactcagcactcagttgctctgtcttaactcgtttgatctcccttgtctctggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
----gcatgatctctgatcttctccctctggacac--acaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
     |  | |   |       ||| | |        |   | |||||| | |  ||| |    ||| ||   | ||    ||||    |||      |||| |   ||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||
caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagtttt----gaaattttatgat----cttctaagctttcgccattttaa---acagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G16070.1 (Glycine max), 3'ss of exon 3
---gcatgatctctgatcttctccctctggacac---acaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
       ||  | | | ||  ||| |||         |   | |||||| | |  ||| |    ||| ||  || || |||||         |||| |   |  |  ||||||||| |||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||||
ctgattggaaattttaactggtccttcttactttttgagggtgatatgatggtaagtttt----gaaattttctgat-cttctaag------ctttagccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTCGGAAACAAAGAAAACTCTGGCAAG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ22344 (Selaginella moellendorffii), 3'ss of exon 2
gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttga-tgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
                                                       | | |  |      |  |  ||| | || ||  ||  |||  |   | ||||| ||||   |||||||||| ||||||||||| ||||||||| ||||    ||  |||||| |
------------------------------------------------------gtaaaagatcaaaccaaacaacttgaacaatttcttactttgaaactttcagAAGCCTGGTACTTGGAGGCTGGCTTGCCAAACAATTGTTGGAGATAAGTCTAATGCTGGCAGG

upper sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ25552 (Selaginella moellendorffii), 3'ss of exon 2
gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaat---gcttcttcatcacttctttggttttga-tgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
                                                     |   |||   || | ||     |  ||| | || ||  ||  |||  |   | ||||| ||||   |||||||||| ||||||||||| ||||||||| ||||    ||  ||||||||
----------------------------------------------------gtaaaagagaatgtcaaaccaaacaacttgagcaatttcttactttgaaactttcagAAGCCTGGTACTTGGAGGCTGGCTTGCCAAACAATTGTTGGAGATAAGTCTAATGCTGGCAAG

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|110402342|gb|EC959914.1|EC959914
EST:     AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAG                         AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
genomic: AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAGgcatgatctc ... tgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
EST: gi|110374024|gb|EC938501.1|EC938501
EST:     GATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAG                         AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
genomic: GATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAGgcatgatctc ... tgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
EST: gi|351021976|gb|FQ437763.1|FQ437763
EST:     AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAG                         AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
genomic: AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAGgcatgatctc ... tgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
EST: gi|110379568|gb|EC944773.1|EC944773
EST:     AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAG                         AAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG
genomic: AAGATCTTCTGAACGAGAGAACAAACACAGAGCTCCGTTATCTGAAGAAGgcatgatctc ... tgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG
       agaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgatctctgatcttctccctctggacacacaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA