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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatacaacaaatgattccccagacttaaactgaatctgccttattgctttaatttatatgcatttttcattaatccaaattatatttctatgaaacagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA

Basic information

species Vitis vinifera
transcript Vv16s0098g00350.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 21
ataatacaacaaatgattccccagacttaaactgaatctgccttattgctttaatttatatgcatttttcattaatccaaattatatttctatgaaacagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA
       ||  | |   |   |   | ||| |  | |||   ||  ||   || |  |   |||| |    ||  | |   || ||||         |||||  | || ||||||||||||||||| |||||||||||  | || |||||| | ||||| || || || ||||  |||||| |||| ||||| |||||||
-----gtaaggattatatatacccccctaatcccactctagttt-ctgaaatagtaaacgcgcatatgatgtt--ttcgtgttttatt--------gcagTGCACTCCAAACTGCTATGCAAGGATTATGAGTGTGGGGCATGACGAGAGCCGTATTGTCCTAATCGCCAAGAAAAATGTCTCTGCCGGCGAAGAGCTAA

upper sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 13
-----------------ataatacaacaaatgattccccagacttaaactgaatctgccttattgctttaatttatatgcatttttcattaatccaaattatatttcta--------tgaaacagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA
                  |  ||  ||||||   ||        |  | |     | ||    | || | | | ||    ||||  |||     |  | ||| ||  |           | |||||||   ||||| |||||||||||||| |||||||||||||| ||||||||| ||||||| || || ||||||||  ||||  || |||| ||||||||||
gtaagtgaaccaaaatagttgtatgacaaattgctcaatttttgtgtattattgttacccctgtactctcactaatggttatttgacatctcatcttactattttcttggttcatgtcaatacagTGTATGCCCAATTGCTATGCAAGGATTATGAGTGTGGGTGATGATGAGAGCCGGATTGTACTCATCGCTAAGACTGATGTGTCTACTGGTGATGAGCTAA

upper sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 22
ataatacaacaaatgattccccagacttaaactgaat----ctgccttattg--ctttaatttatatgcatttttcat-taatccaaattatatttc-tatgaa-acagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA
 | |  ||||  |   ||     ||| |   ||| ||     || | | | |   | | |  | |    | |  | || | | |     | |  ||| | | || |||||||   || || |||||||| |||||||||||||| |||||||| |||||| ||||||| || ||||||||||| || || | ||| || |||||| |||
gtgagtcaacctaaacttgaattgacattttctgtatatctttgtcctctcggattctcaactctggataatagttatcttacctgttctttggttcatgttaatacagTGTATGCCAAATTGCTATGCCAGGATCATGAGTGTTGGTGACGACGAGAGCCGGATTGTACTCATTGCTAAGACTAACGTGGTTGCCGGTGATGAGTTAA

upper sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 22
ataatacaacaaatgattccccagacttaaactgaatctgccttattgctttaattt---atatgcatttttcat-taatccaaattatatttc-tatgaa-acagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA
 |||  ||||  |   ||     | | |   ||| |  |  ||     ||   |||    | |     |  |||| | | |     | |  ||| | | || |||||||   || || ||||||||||||||||||||||| ||||| || |||||| ||||||| || || |||||||| || || ||||| || |||||| |||
gtaagtcaacctaaacttgaattggcattttctgtacatcactgtcatctcggattctcaacacaggatagtcatcttacctgttctctggttcatgttaatacagTGTATGCCAAATTGCTATGCAAGGATCATGAGTGTCGGTGATGAGGAGAGCCGGATTGTACTCATCGCTAAGACTAACGTGGCTGCCGGTGATGAGTTAA

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|30133456|gb|CB918795.1|CB918795
EST:     TAGTCGATGCTACAGATAAAGGAAACATTGCCCGCCTAATCAACCACTCA                         TGTGCCCCNCA-CTGCTATGCGAGGATCATGAGTGTGGGTGACGATGAGAG
genomic: TAGTCGATGCTACAGATAAAGGAAACATTGCCCGCCTAATCAACCACTCGgtaagtcatt ... tatgaaacagTGTGCCCC-CAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttaatttatatgcatttttcattaatccaaattatatttctatgaaacagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA
                        cattaat  putative branch site (score: 3)
                                       tatttct  putative PPT
     ttaatttatatgcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatacaacaaatgattccccagacttaaactgaatctgccttattgctttaatttatatgcatttttcattaatccaaattatatttctatgaaacagTGTGCCCCCAACTGCTATGCAAGGATCATGAGTGTGGGTGACGATGAGAGCAGGATTGTTCTTATTGCTAAGACCAATGTCGCTGCTGGCGATGAGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - -acaacaa
- - - - - - - - ttcccca
- - - - - - - - - - - - - - aaactga
- - - - - - - - - - - - - - - - - - tctgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatccaa