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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg...

Basic information

species Vitis vinifera
transcript Vv16s0050g02180.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagc----tctttctcttggagtttctagttccttaagatg--tagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg
|||| ||||| |||||||||||||| || ||||||||||| || ||||| ||||| ||| |||||| ||||||||||||| |||||||| || |||||||| | || || |||| | | || | | ||| | |||| || | || || | || | | |||
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTTCGAGAAGGTTCTGATGGCATTATGCTTTCTGGGGAAACTGCACACGGAAAgtatgtgatatccttttcttatgcatagatgatcactcacatgatcaaaatttaataactaaagtaggctgattttttttattttttattcagtca-tact-----

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G152686_T01 (Zea mays), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaaga--tgtagctggagataatgggagcaccttggttcatattgggaaaaaaat-gtttggcacttgagg
|||| ||||| |||||||||||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||| | | | ||| || | | || | | || | | | | | | ||| || | | | || | | |||||
TTCATCCAACTCCAACCCGAGCAGAAGTTTCAGACATTGCTATAGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCAGGAGAAACTGCACATGGGAAgtatgtcacatgttttg---ctttttgctcaaaagaaattgatgttattagttgttagctaagggtggctccaagagttagcaagccagctcataacttgcca

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G37210.1 (Glycine max), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg-
||||||||||||||||| |||| |||||||| || ||||| |||||||| ||||| ||| |||||||| | ||||||||||| ||||||||||| |||||||||| | || | || |||| | || || |||| | | | | |||| || | | | | | | | |
TTCACCCAACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCACGGAAAgtaagtaataattccatgccttgaagtgtcctattaccttggcaggcgatattctca-tatttgagttcttacaaaggacaggaaaatcacaatcaaatgc

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA20G30430.1 (Glycine max), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagc------tctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg-
||||||| ||||||||| |||| |||||||| || ||||| |||||||| ||||| ||| |||||||| | ||||||||||| |||||||||||||||||||||| || | || ||| || | || | | | || || ||| | | | |||| || | | | | | | || | |
TTCACCCGACACCAACCAGAGCCGAGGTATCCGATATTGCAATTGCTGTTCGAGAAGGTTCTGATGCAATAATGCTTTCTGGGGAAACTGCTCATGGAAAgtaagtaataattccatgcctcaaagtgtccaattacct------tggcaggtgatgttctcc-tatttgagttcttacaaaggacaggaaatatcacaatcaaatt

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA09G23150.1 (Glycine max), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagc---------tctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg
|||||||||| |||||| ||||||||||||| || || || |||||||| ||||| ||| |||||| | | ||| | ||||||||||| |||||||||||||||| || ||| | | ||| || | || | | | | || | | |||| | | | || || ||| | ||| ||||
TTCACCCAACTCCAACCAGAGCAGAGGTATCGGATATAGCAATTGCTGTTCGAGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaaatagttttccttcccctatagtgtccaattattcagt---cactttatattactagtagcatgtatatgactttttggcaaa-----tctgggctttgaa-

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G28980.1 (Glycine max), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggaga-taatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg-
|||||||||| |||||| |||||||||||||||| || || ||||| || || || ||| |||||| | | ||| | ||||||||||| |||||||||||||||| | | || | ||| | | | | || | | || | ||| | | | | | || ||| ||||
TTCACCCAACTCCAACCAGAGCAGAGGTATCAGATATAGCAATTGCAGTTCGTGAAGGTTCTGATGGAATAATGTTGTCTGGAGAAACAGCTCATGGAAAgtaagtaaatagttttcctgcgcctaaagcatccaattactttgaaaggctggtcttagaagtttgtgac-tggtaaggggaccat-tttaccactaagtcc

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G28980.2 (Glycine max), 5'ss of exon 8
--------------------------------------------------------------------------TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg
|||||||||| |||||| |||||||||||||||| || || ||||| || || || ||| |||||| | | ||| | ||||||||||| |||||||||||||||| | | || | |||
AGAGATAATCAACTTGTGTCGTAGCATGGGAAAGGCTGTTATTGTGGCAACAAATATGCTAGAAAGCATGATTGTTCACCCAACTCCAACCAGAGCAGAGgtatcagatatagcaattgcagttcgtgaaggttctgatggaataatgttgtctggagaaacagctcatggaaagtaagtaaatagttttcctgcgccta--------------------------------------------------------------------------

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 5'ss of exon 8
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagct-ctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg----
|||| ||||| |||||||| |||||||| ||||||||||| || ||||| |||| ||||||||||| || |||||||| |||||||||||||| |||||||||| | | |||| || | || ||| ||||| ||||||| | | | || ||| | | || | ||||||
TTCATCCAACTCCAACCCGGGCAGAGGTCTCAGACATTGCTATCGCTGTTAGAGAAGGTGCTGATGCGGTAATGCTTTCAGGAGAAACTGCTCACGGAAAgtaagtggcagtatctt----ttcatgtactctattgatttagctt---ataatggcattgaat-gtttattatatgcatgaatctcaactttacttgatatcag

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg------
|||||| || || || |||||||| || |||||||| ||||| |||||||| || ||||| |||||| |||||||||| || ||||| ||||||||||||||||| | | ||| || | | | | | | | || | || || | || ||| | | || | ||||||
CTCACCCTACGCCCACACGAGCAGAAGTCTCAGACATAGCCATCGCTGTCCGTGAAGGTGCGGATGCAATTATGCTTTCAGGGGAAACCGCTCATGGAAAgtaagcgcgattaaaccagtgcactatctctcgacagttt--ttttttctgcttgaagtaaatt--tttgtgtttcgaatatcgtatt--actgttgaggacgatc

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 7
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatggg--agcaccttggttcatattgggaaaaaaatgtttggcacttgagg
|||||| || || || ||||||||||| |||||||| || ||||| ||||| || ||||| || ||||||||||||||||| ||||| ||||| |||||||||| | || ||| |||| | || | || | || | || | || || ||||| | | | || | | |
CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacctttggaatttgttgatagtcttctttaatatcatctaagctcatagcccagtaactgccaaaattttggggcatcag-gcttatcgtcagtg-

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|110361781|gb|EC925279.1|EC925279
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAA                         GTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctt ... ttacatgcagGTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
EST: gi|30134905|gb|CB920243.1|CB920243
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAA                         GTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctt ... ttacatgcagGTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
EST: gi|110698146|gb|EE075377.1|EE075377
EST:     CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAA                         GTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctt ... ttacatgcagGTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
EST: gi|30321651|gb|CD004913.1|CD004913
EST:     CGAGANGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAA                         GTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA
genomic: CGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctt ... ttacatgcagGTTTCCCTTGAAAGCTGTGAAAGTCATGCATACAGTTTCCTTAAGAACTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACCCAACACCAACCCGAGCAGAGGTATCAGACATTGCCATTGCTGTCCGAGAGGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCTCATGGAAAgtaagctctttctcttggagtttctagttccttaagatgtagctggagataatgggagcaccttggttcatattgggaaaaaaatgtttggcacttgagg

- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa