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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTCAGCAGGAAATCATGCACAAGGGGTTGCATTAGCTGCAAAGCGACTTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgttgtttggtgttgctcttgttgcttgtttttacttatgattgtatcttcacaattttgattttgaacttctggactttttatgtgtacag

Basic information

species Vitis vinifera
transcript Vv08s0007g04310.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G07340.1 (Glycine max), 5'ss of exon 2
CTCTTCAGCAGGAAATCATGCACAAGGGGTTGCATTAGCTGCAAAGCGACTTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgttgtttg---gtgttgctcttgttgcttgtttttacttatgattgtatcttcacaattttgattttgaacttctggactttttatgtgtacag---------------
||| || || || |||||||| ||||| |||||||| ||||| ||| |  |   ||||| ||| ||||||||||||||||| ||||| || ||||||||||| | || ||||||    || | | | |  ||| |||| | |   | | ||| ||||     ||    || ||||  |   |    | | | | | |                   
CTCGTCTGCTGGCAATCATGCTCAAGGAGTTGCATTGGCTGCCAAGAGGTTGAATTGCAGTGCGGTGATTGCTATGCCTGTCACCACTCCGGAAATCAAGgt-gtgttttgtttatatgtttagttttgcttgtttgtctgtttctttaattatatccgaggaaaagagaatttgttcaatttagttatgtgtttttgtttcttgtgacattgcag

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G10050.1 (Arabidopsis thaliana), 5'ss of exon 2
CTCTTCAGCAGGAAATCATGCACAAGGGGTTGCATTAGCTGCAAAGCGACTTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgttgtttggtgttgctcttgttgcttgtttttact-tatgattgtatcttcacaattttgattttgaacttctggactttttatgtgtacag
||||||||| ||||| ||||| ||||| ||||| ||| |||| |    ||| || |||| ||||||||||| |||||||||||| || ||||| || |||||    |    |||   | |  |||  |  ||||   ||| | | |||| || |  |   | |    |                               
CTCTTCAGCTGGAAACCATGCTCAAGGAGTTGCTTTATCTGCTAGTAAACTCGGCTGCACTGCTGTGATTGTTATGCCTGTTACGACTCCTGAGATAAAGgtattttccatttttaagct-ttctcatgtcttgaagttagtatctgatggtgttctgggattgaaaacag----------------------------

upper sequence: Vv08s0007g04310.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ38617 (Selaginella moellendorffii), 5'ss of exon 2
CTCTTCAGCAGGAAATCATGCACAAGGGGTTGCATTAGCTGCAAAGCGACTTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgttgtttggtgttgctcttgttgcttgtttttacttatgattgtatcttcacaattttgattttgaacttctggactttttatgtgtacag
|||||| || ||||| || || ||||| ||||||||  | ||  |  | ||||||||| |||| || || || |||||||| |||||||| |||||||||||   ||  | |    |   |   |  | |       ||| |     ||| |                                              
CTCTTCCGCGGGAAACCACGCGCAAGGAGTTGCATTGTCCGCTCAAAGGCTTGGTTGCGATGCAGTCATAGCGATGCCTGTCACCACACCAGAAATCAAGgtaaggtcctttcgttttcagagataatcgaacagcgttattgtgagttgcag---------------------------------------------

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|352782068|gb|FQ469366.1|FQ469366
EST:     TGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCCTGAAATCAAG                         TGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCG
genomic: TGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACC-TGAAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCG
EST: gi|351028931|gb|FQ434932.1|FQ434932
EST:     TGGTTGCAATGCTGTGATTGCTATGCCTGTTAC-ACACCTGGAAATCAAG                         TGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGGTCTTG
genomic: TGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTG-AAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTG
EST: gi|352769243|gb|FQ471392.1|FQ471392
EST:     TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAG                         TGGAAGTCTGTTGAGAGAATGGGTGCCACAGTTGGTCTT
genomic: TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTT
EST: gi|351025411|gb|FQ435103.1|FQ435103
EST:     TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAG                         TGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCC
genomic: TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCG
EST: gi|34551096|gb|CF519290.1|CF519290
EST:     TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAG                         TGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCG
genomic: TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTTGAGAGATTGGGTGCGACAGTTGTTCTTGTGGGGGATTCG
EST: gi|352764055|gb|FQ467625.1|FQ467625
EST:     CTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCCAAAATCAAG                         TGGAAATCTGTT
genomic: TTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgtt ... atgtgtacagTGGAAGTCTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTTCAGCAGGAAATCATGCACAAGGGGTTGCATTAGCTGCAAAGCGACTTGGTTGCAATGCTGTGATTGCTATGCCTGTTACCACACCTGAAATCAAGgttgagtgttgtttggtgttgctcttgttgcttgtttttacttatgattgtatcttcacaattttgattttgaacttctggactttttatgtgtacag

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