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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA

Basic information

species Vitis vinifera
transcript Vv18s0001g07520.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G10060.1 (Glycine max), 3'ss of exon 12
gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA
                                    |     || |    | |    |||  | ||  |    |  ||    |  ||   |  | ||| |   |||||   | |||||| ||||||||||||||||||||||||| || |||||||||||| ||||||||||||  || ||  |||| || ||| ||||  || || |||| || |
-----------------------------------gtgagcattattggttcacatgcttaatgttcttggactttctgatgtgtatttttctgattagcatgtttcttcatgcagAATATTGTAGCTGATATGCGCAAGGTTTTGTCTAAAAATCCTCAAGTAGAGCAGCAAAAATTACACCGAAGGGTTTTTTTGGAGAATGTCAATCCTGAAA

upper sequence: Vv18s0001g07520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G10060.1 (Glycine max), 3'ss of exon 11
gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA
    |||||||  | |||||| |  | | |   || |            ||  || ||||  |  ||  | |||  ||               | ||| |   |||||   | |||||| ||||||||||||||||||||||||| || |||||||||||| ||||||||||||  || || ||||| || ||| ||||  || || |||| || |
----gtgagcatta-ttggttcacatgcttaaaaaatg-----------ctctaggactttctgatgtgcatttttct---------------gattaacatgtttcttcgtgcagAATATTGTAGCTGATATGCGCAAGGTTTTGTCTAAAAATCCTCAAGTAGAGCAGCAAAAATTACACAGAAGGGTCTTTTTGGAGAATGTCAATCCTGAAA

upper sequence: Vv18s0001g07520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G10050.1 (Glycine max), 3'ss of exon 11
gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctct-----tttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA
                  ||   | | | | ||   || |  ||||    | | | |||   |  |||  || || | |||| |||  |     || ||||||     |||||   | |||| | || ||||||||||||||||||||||  | |||||||||||| |||||||| |||  ||||| ||||| || ||||| ||  |||| |||||||| |
------------------gtgagtattcttgtct-ttaaaaattgt----tcagggact-attgatgg--ctatctcatcatctgaaaacaaaagtaatctctcctagtttctttatgcagAGTATTATAGCTGATATGCGCAAGGTTTTGGCAAAAAATCCTCAAGTAGAGCAGAAAAAATTGCACAGAAGGGTTTTTCTAGAGAATATTGATCCAGAAA

upper sequence: Vv18s0001g07520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G10050.1 (Glycine max), 3'ss of exon 9
gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA
                  ||   | | | | ||   || |  ||||  |      |   || |     |    ||   | |    |  | |    |   ||  |||||   | |||| | || ||||| ||||||||||||||||  |||||||||||||| |||||||| |||  ||||| | ||| || ||||| ||  |||| |||||||| |
------------------gtgagtattcttgtct-ttaaaaattgttcag--ggactactgatagctatgtcatcatctgaaaacaaaagtaacatctcctaatttctttatgcagAGTATTATAGCTTATATGCGCAAGGTTTTGGCCAAAAATCCTCAAGTAGAGCAGAAAAAATTGCACATAAGGGTTTTTCTAGAGAATATTGATCCAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA
                   atttgat  putative branch site (score: 5)
                                  ttatctcttttct  putative PPT
                ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagcaaaaattggtttatctacctctcaactagatcttgtctacttaagcacttggttttggtcctttcccttcatttgatgaattgggttatctcttttctggttacagAATGTTGTAGCTGATATGCGCAAGGTTTTATCCAAAAATCCTCAAATAGAGCAGCAAAGGTTGCATAGAAGAGTGTTTCTGGACTATATCGATCCAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG