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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt...

Basic information

species Vitis vinifera
transcript Vv11s0016g00700.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 5'ss of exon 2
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcat-atagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatg-tttattctttcgtttgtcaacactt
|||||||| ||| | | |||||||||||||||||| |||||| | |||||||||||||||||||||||  ||| |  ||   ||| |  |||||| ||| | ||    |  | || ||     |||  | | || ||| |||   |||| |    ||    |  
ATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGTgtgagtcccattagggattctttttattttttttattttcttttcttcgtatgcttgaaaatgca-taagttcatgctttggactttagggcatcttttcc-

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattc-tttcgtttgtcaacactt-
|||||||| ||  | ||||| || ||||||||||| |||||||||||||||||||| ||||||| ||| |     |    ||||   || |||  || |     |    || |   |  | || | || ||||  |  |  |||    | ||    || | || 
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtcacctgttttgccctgttt--atgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 2
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtg-tgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt-
|||||||| ||  | |||||||| ||||||||||||||||||||||||||||||||||| |||| |||||   |      | ||  |||  | | || |  |  |   || | | |||   |    |||| ||||| |   ||               |  || 
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttc--taaattcttcttttaagaacatctacataaaatatggcttttc

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 3
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtg-tgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt-
|||||||| ||  | |||||||| ||||||||||||||||||||||||||||||||||| |||| |||||   |      | ||  |||  | | || |  |  |   || | | ||| |   |  |||| ||| |       ||  |    | |      |  
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttccaaat--tcttctttaagaacatctccataaaatatggcttttct

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 3
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt-
||||||||||||||||||||||||||||| ||||| |||||||| ||| ||||||||||||||||||||| | ||||||||||| || |  |||  ||    |       || |  |  | ||    |||||||   || ||  |||  ||  || |   |  
ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGTgtgagtgtta-atagacattttattttcatttttttaaaattaacatattcgactgttcttttgtttattttgatttaatcatttttttcttccagtttag

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G17200.2 (Glycine max), 5'ss of exon 2
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt----
||||||||||||||||||||||||||||| ||||| |||||||| ||| ||||||||||||||||||||| | ||||||||||| || |  |||  ||   || ||   ||    | |  |||| |  ||||||   |||| ||||   ||| |   || ||    
ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGTgtgagtgtta-atagacattttattttcatttttttaaattagtaacttcaactgttctttgtt--tattttg-atttagtcttctttttttttccagtttagc

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ13606 (Selaginella moellendorffii), 5'ss of exon 2
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacatt--ttcttcttttttgattc-----ttttcgtgtgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaac--actt----------------------------------------------------------------------------------
|| ||||| ||    |||||||||||||| || ||||||||| ||| | | || |||||||||||||||   |       ||  || |||||||||| |       ||   || | | ||   || |||   | |  ||||   ||| | |||| | ||||  |   ||||                                                                                  
ATTGAGCCAATTCCAAGTGGAAATCTGCCACCAGGGTTTGATGCAACTTCTTGTCGCAGTGTgtgagtgcttttctttttttcttttttcttttttgttgtaccaattcaggtatctgttttcttttttcaatttcctttttcttttttccttttggttgtttattaacttaaaaactatgctgagcttgggccgtcattgctttggttgcggaatgattttgtttctagtctgatgttcattcctgctgcag

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|110685954|gb|EE063126.1|EE063126
EST:     TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT
genomic: TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtca ... ataattgcagGTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT
EST: gi|156737274|gb|EV241395.1|EV241395
EST:     TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT
genomic: TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtca ... ataattgcagGTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT
EST: gi|294966632|gb|GW839623.1|GW839623
EST:     TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT
genomic: TTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtca ... ataattgcagGTATGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattctttcgtttgtcaacactt

- - - - - - -  AGTGGA