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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG

Basic information

species Vitis vinifera
transcript Vv01s0010g02760.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 10
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagta-acaaatctttgttgatt---tagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
                                                                              |||  | |  |  | |||  |  | ||  | | |  | | ||     | ||| |   ||  |   | |  ||    |      |||||||  | |    |||| || | | | ||||| || ||  |   |||||| ||||  ||||||||||||||| ||||||||||||| || ||||||||||| ||  | || ||||
-----------------------------------------------------------------------------ctttaaaacattcaagggaagtgaattttcacattttcgatgtcaacactattgtt--gttccaagtatgattgtacatgttcctctttgtaaactgagcagGGAAATACTTCAAAACCTGAAGGATTGGCTGAAATCATTAAAGCTGGAGCAATGGGTTTGAAGCTGCATGAAGATTGGGGAACTACCCCATCCGCGATAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 11
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatct-gttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatc--tttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
                            |  ||| ||| |||| |    |||||||  | | | |  |   |   |  |||   ||| |||      | |||  |||   | |||| |     | | ||  ||  |      | |   || || |||    ||  ||| ||| || ||||||| ||||||||||| || |  || ||||||||||| ||||||||||| ||||| ||||||||||||||||||||||||||||| || ||||||||||
-------------------------gtctgttttctttcttttgttttgttcacata-taatgcttgttttgtgtagttttttttctagtttgttttcctcgtgtta---agtgccgaacctctagaaaacctcgacgaaggtttaaagtcaattaaatcctccatttattgcttcagGGGAATAGTGCCAAACCTGATGAACTGCATGAAATAATCAGGGCTGGAGCTATGGGACTGAAGCTGCATGAGGACTGGGGAACTACACCGGCTGCAATAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 10
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatg--cctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
||||| | | || ||       ||||  |||| | | ||| || |   ||||   | ||||   |||  |   |    | | | ||  |       ||     |||| | |||    || |   |  |  |  | || |        ||  |   ||       || |||| ||||||| |  ||| |||| || || |  |||||||| ||||| | ||||||||||||||| ||||||||||||||||||||||||| |||||| ||||||||||
gtgtgttgcctttttga-----tatatcttctgtttatgtcttgt--ttttc---ttgtcatattgcaaagttatttttcttgttcctt------gctcaatgttatgtgatggatttaagacctctctttcttcaaataattcaatttactttcta-------ttggttgctttagGGAAGTAGTTCCAAGCCTGATGAACTACATGACATAATCAAGGCTGGAGCAATGGGACTGAAGCTGCATGAGGACTGGGGAAGTACTCCCGCTGCAATAG

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 10
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
             | ||   | | |  | ||| |  |  || |||    ||    | | ||   |||  |   |    | | | ||  |   | |   |  |  |||| ||  ||||  |   | ||| |   |||||   |    | |  |          || |||| |||||||||  ||| |||| || || |  || ||||||||||| | ||||||||||||||| |||||||||||||||||||||||||                  
------------gtgtgttgccttttctctctcttctgtttatatgttatttttcttggcatattgcaaagttatgtttcttgttcaatgttacgtgatgcacctatagaagacctatctttcttcaaat---aagtcaattaaactttcta----------ttggttgctttagGGGAGTAGTTCCAAGCCTGATGAACTGCATGAAATAATCAAGGCTGGAGCAATGGGGCTGAAGCTGCATGAGGACTGGGGAA------------------

upper sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
                                                                    |  | | |  |||     || |   |   | |   ||||  |     ||   |  || | ||| ||| |||    |   ||||   ||   ||| |||||     |||| || |  || |||||    | ||| | | | ||| |   |||||||||||||||  ||||||||||||||||||||||||||||||||||||||||||
--------------------------------------------------------------------gtgggatatgtttcttcttgatactgatatccttgttatcca---tgtactcatctgtatttc-gaactct----tacggttagcaaatgtatcgttgtt-----agGGAAATACAGCTAAACCGTTAGAGCTTCGTCACATAGTGGAGGCTGGAGCAATGGGATTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG

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|161720992|gb|FC070359.1|FC070359
EST:     TGCTGCAATCAACTGATGACCTGCCACTGAATTTTGGTTTCACAGGAAAA                         GGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCA
genomic: TGCTGCAATCAACTGATGACCTGCCACTGAATTTTGGTTTCACAGGAAAAgtgtgcttca ... gttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG
                                        tctttgtt  CT-rich tract
                            ttaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcttcattatttgcaacttatagtttctttgtttgttttatagctttcacatggtcaagatgctgaagcacacatttggatctgttgaaggacttcgaattatataatgcctaggtagttgcaattctgaagtctcctctcttgttaagtaacaaatctttgttgatttagGGGAACAGTGCCAAACCAGACGGGCTACATGAAATAATTAGGGCTGGAGCAATGGGTCTGAAGCTGCATGAGGACTGGGGAACTACTCCTGCTGCAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC