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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtatttctcagaacggggttctgtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG

Basic information

species Vitis vinifera
transcript Vv02s0025g00650.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 12
gttggtatttctcagaacggggttctgtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG
||  ||||  |  |  ||  |  ||| ||  |  |  || |      | |  || ||| ||| |   ||  | |   ||||||||||||||||||||| || ||||| ||||| |||||  | || ||  | || |||   |||||  ||
gtcagtat--cataagacatgaatctatg--tcaacccaaagaactctttggttaact-cag-tagtctgctgtgtgacagAACCTGTGCACAACAGCAGCGTATCGTCCAGTGAGGGAACTGATCCAAAAGGAAAGAAAGAAGGAACTG

upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G02270.1 (Glycine max), 3'ss of exon 9
-------------------------------gttggtatttctcagaacggggttctgtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG
                                    ||  |      || |  |    |||   | ||| ||| ||  | || || ||||  ||| |  ||  | ||| |||||| |||||||||| ||||||||  |||| || || |||||||| |||||||||||||| |||  | ||
gtatatacaattttctaattatcgtgtcacaaactataaatgcttttacagcttctgatgcgcaggtgcctaa-cacat-tttttcactgttgctaa--ttgctaaatgcagAACTTGTGCACAACTGCTGCTTACAGGCCTGTTAGAGAGTTAATTCAGCAAGAGAGACTAAAGACTCTG

upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G02260.1 (Glycine max), 3'ss of exon 14
-------------------------------------gttggtatttctcagaacggggttctgtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG
                                          |||     |  | | | || |    ||   ||| |       | |  || | |     | ||| | |  |    ||||| |||||||||| |||||||||||||| || || ||| |||| |||||||||||  | |||  | ||
gttgctgctattcttttatattgttcacattggatataacactatcgtgtaacaagtgctttttgttttccgtgcttttaattatatcatttattcattgtcaacctgtccatcgtagAACTTGTGCACAACTGCTGCTTATCGGCCTGTTAGAGAGCTAATTCAGCAAGAGAGGATAAAGAGTCTG

upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G37290.1 (Glycine max), 3'ss of exon 14
----------------------------gttgg---tatttctcag--aacggggttctgtgctttgatgcataatcaggtgttc--ttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG
                             ||||   ||  | |||   |||  |    | |  ||   ||     | | || | |  || | |     | ||| | |  | |  ||||| |||||||||| |||||||||||||| || || ||| |||| ||||||||||| || |||  | | 
gttgctactattcttttatattgttcacattggacataactatcatgtaacaagtgctttttgttatctgtgcttttaagtatcccttttattcattgtcaacctgtccattgtagAACTTGTGCACAACTGCTGCTTATCGGCCTGTTAGAGAGCTAATTCAGCAAGAGAGGCTAAAGAGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG
                                            ttttaat  putative branch site (score: 3)
                                         ctttttt  CT-rich tract
                                     ttaacttttttaatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtatttctcagaacggggttctgtgctttgatgcataatcaggtgttcttgactgcagcttaacttttttaatacagAACCTGTGCACAACAGCTGCTTATCGGCCAGTCAGGGAGTTAATACAGCAAGAGAGACTTAAGGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA