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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctccatttttatttttatgtattttagttttttccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT

Basic information

species Vitis vinifera
transcript Vv01s0026g00610.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00610.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G04270.1 (Glycine max), 3'ss of exon 9
gtgagttctccatttttattttta---tgtattttagttttttccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT
|| ||  ||| | |||  ||| |    | | || |  | |||  ||||||     | |||||   |||              ||| ||||  ||| |||| ||| |  ||||||||||||| || || || ||||| ||||| ||  |||||||||| |||||||||||||| || |||||||| |||||||||||||
gtaagc-ctctactttagtttctcatctttgttctgttgtttgtcttttctatacactgaca---gat--------------tttatctcattcttagTTAGAACTTAGTTATAATCCCATTGGACCAGATGGAGCCAAGGCCTTGGCTGAAGTTCTCAAGTTTCATGGGAACATAAAAACCCTTAAGCTTGGTTGGT

upper sequence: Vv01s0026g00610.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G03410.1 (Glycine max), 3'ss of exon 11
gtgagttctccatttttatttttatgtattttagttttttccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT
|| ||  ||| |   ||||||    ||   | |  ||| | || ||   |||  |     |   |   | ||  |    ||| ||||  ||| |||| ||| |  ||||||||||||| || || || ||||| ||||| ||  |||||||||| |||||||||||||| || |||||||| |||||||||||||
gtaagc-ctctacagttattta---gttcctcatctttgttctgtt---gtttgtcttttc---tatacactaacagattttatctcattcttagTTAGAACTTAGTTATAATCCCATTGGACCAGACGGAGCCAAGGCCTTGGCTGAAGTTCTCAAGTTTCATGGGAACATAAAAACCCTTAAGCTTGGTTGGT

upper sequence: Vv01s0026g00610.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G10510.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgagttctccatttttatttttatgtattttagttttttccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT
|| ||| |   |      | |      || || | ||  |  ||| ||  | | |   |  | |    | ||  | ||||   | | || ||||||| ||  | ||||||||||||||||| || || ||||| || || ||||||||| |||| ||||| ||||| ||  | || || || || ||||||||||
gtcagtgccaaaaacccttctc-----atctttgattccttgtttacgtataactagtatgataatgacactaccactctcaatatttc-ctcagTTAGAGGTTGGTTATAATCCCATAGGACCAGACGGAGCTAAAGCATTATCTGAAATTCTCAAGTTCCATGGAAATGTAAAGACGCTCAAACTTGGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT
        ggttaat  putative branch site (score: 4)
                 caacagatcctctctc  putative PPT
          ttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctccatttttatttttatgtattttagttttttccttttcgggttaatgacaacagatcctctctctctctctttctctctctctcagTTGGAATTAGGTTATAATCCCATAGGGCCTGAAGGAGCAAAGGCTTTATCTGAAGTTCTGAAGTTTCATGGGAAGATCAAAACCCTGAAGCTTGGTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC