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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcactcaatcaagatgcccatatttctatgttcctgttttggtgggtttccaaaatgtgcaaaaagtagaatctcatacactacactaaaatttt...

Basic information

species Vitis vinifera
transcript Vv12s0059g01290.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G38820.1 (Glycine max), 5'ss of exon 4
GATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcactcaatcaagatgcccatatttctatgttcctgttttggtgg-gtttccaaaatgtgcaaaaagtagaatctcatacactacactaaaatttt----------
||||||||||||||||| || || || |||||||| || ||||||||||| || |||||||||| |||||||||   || |||          || |||        |||| || ||||  ||||  |   ||  | |   |   || |  |     |  |     |||           
GATCGCATTATAGCTCGCCTACAGCAGCCATATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAGgttgg---cttaatt--------tattttttccccccactgtgttagtggcatttctcattggtatacattttcttattttgtgtttcattcctgtgtttgctaaatgaag

upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G28950.2 (Glycine max), 5'ss of exon 5
GATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcactcaatcaagatgcccatatttctatgttcctgttttggtgg-gtttccaaaatgtgcaaaaagtagaatctcatacactacactaaaatttt----------
||||||||||||||||| || || || || ||||| || ||||||||||| || |||||||||| |||||||||   || |||          || ||||     |  ||| || ||||  |||   |   ||  | |   |   || | ||     |  |     |||           
GATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAGgttgg---cttaatt--------tatttttcccccctattgtgttagtggcatttgtcattggtatacattttcttattttatgtttaattcctgtgtttgccagatgaag

upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 5'ss of exon 4
GATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcactcaatc--aagatgcccatatttctatgttcctgttttggtgggtttccaaaatgtgcaaaaagtagaatctcatacactacactaaa--atttt-------------------
|||||||| || |||||||| |||||||| ||||| ||||||||||||||||| |||||||||| ||||||   |||  | ||   |   |      |  | |  |  |||  ||| ||     ||  || | |||| ||     || |  | |  |||   | ||    |||                   
GATCGCATCATTGCTCGTCTCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAGgtgattcatgccattttatactatttgcaactttgaggaccttatttagta----tctgaagt-tgcacaactggaaaacgaagatgctatgtttaatggctttgttctgctttgtttttcag

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|349826040|gb|FQ415845.1|FQ415845
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110365436|gb|EC928421.1|EC928421
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110386241|gb|EC950822.1|EC950822
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|351019910|gb|FQ439727.1|FQ439727
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|161721680|gb|FC069810.1|FC069810
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110401450|gb|EC968060.1|EC968060
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110413892|gb|EC979707.1|EC979707
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110374601|gb|EC939475.1|EC939475
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110382053|gb|EC938357.1|EC938357
EST:     TTCAGCAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
EST: gi|110374049|gb|EC938544.1|EC938544
EST:     TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAG                         AAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG
genomic: TTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcact ... gtttgtacagAAACAATTTTCAGAATTATTGATGAAGGCTGCAAGTGATTATGGTGCCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGgttggtcactcaatcaagatgcccatatttctatgttcctgttttggtgggtttccaaaatgtgcaaaaagtagaatctcatacactacactaaaatttt

- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaa