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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

Basic information

species Vitis vinifera
transcript Vv14s0060g01680.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttca-gATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                                                ||       ||  |||||| |  |  | |  | |       | || || | |   ||||     |  ||| | | || ||| | | | | |||||||| |||||||||||||||||||| || || | ||| ||||| |||||||||||||||||| | || |||||||| |||  ||||||| | || 
---------------------------------------------------------------------------------------------------------------gtaagcagaggtattactttcgtaccgaaagttgt-------ctttagttattg--ttgttgtactaatttacttgtttttcatatgaagGTTGTTCTCATGTGGAACAAGTAAAGATGGAGATTCATATTTAGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGGTTTCGTAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                              || | | | ||    |     | || | |  |        | |  | ||  |  ||    |||| ||   |       | ||   ||||| || | |       || |||||||| |||||||| || ||||| || ||||| | ||||||||| |||||||||||||||||| | || |||||||| |||  ||| ||  | || 
----------------------------------------------------------------------------------------------gtaagaatagttaggttggctcttatttttatcaccaaagttagttctagttttca----atttttactgaggaaacaatttgccttttcttcatgtga-----agGTTGTTCTCATGTGGAACTAGCAAAGAGGGAGACTCCTATTTGGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGATTCCGTAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 12
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                              || | | | |     | ||  | || | |           | |  | ||  ||    ||  |||   ||||||     | | |  |||||||    |  | |  || |||||||| ||||||||||| ||||| || ||||| | ||||||| | |||||||||| ||| ||| | || |||||||| |||  ||| ||  | |||
----------------------------------------------------------------------------------------------gtaagaatagataggttatctcttatttttaccaccaaagttagttctagttgtttcaattttt---actaatgaaacaatgtgcttttcct----tcgtgtgaagGTTGTTCTCATGTGGAACAAGCAAAGAGGGAGACTCATATTTGGTTCAGTGGAATGAAAATGATGGATCTATCAAGAGGACATATTCTGGATTCCGTAAG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 15
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                             || ||   | |    |     || || |   || | |  ||  ||        ||| |   |  | |  ||   |  || |  || |   || |||| ||||    |    | || | | ||| || || |||||||| |||||||||||||| || |||||| | |||||||||||||||||||||||||| || ||||| || || ||||| || ||||| 
---------------------------------------------------------------------------gtaagttggatatgg-atgagggtaattattcctttacagtatcatgcttggtgcttggt-ggacgtttaagatgtattatattaaagtttcttatgacattttc---caaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGATTCAGAAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                  |   ||   |     |     |||   | ||  ||||   | ||||    ||| |    |   |||||    || |||   | | |||  |    | |||  |||    ||  | ||  || |  | | |  ||| |||| ||||| ||||| ||||||||||| || || ||| | |||||||||||||||||||||||||| || ||||| || || |||||||| ||||||
-----------------------------------------------------------------gtaagaaggatttgggtgcggataag--tatttaagtttcatgttcaatggataat----tgaatttga---gatgtattaaataaaaccgt----attaacatgt---cttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtc--ttttcataccat-actgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                      ||||  | | | | | ||    |  | || |  | || ||   |   |  ||   |||  |  ||   |  || |  || |   || ||||  |||    |    | || | | ||| || || |||||||| |||||||||||||| || |||||| | ||||||||||||||||||||||| || || ||||| || || ||||| || ||||| 
--------------------------------------------------------------------------------------gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaat-ggataattaagatgtattatattaaagtttcttatgacactttc---caaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaa-atatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                 |       || | | |   | |   | || |      | ||| | |    | || || || |||   | | |||  |  ||||  || | |  || ||| | | |  || ||  | | ||| |||| ||||| ||||| ||||||||||| || || ||| | ||||||||||||||||||||| |||| || ||||| || || |||||||| ||||||
--------------------------------------------------------------------------------gtaagaaggatttgggtgcggataagtatttaagtttca-tgttcaatggataattaagatgtattaaataaaaccgtattaac--atgtcttcctatttgtcttccattatttctat-agACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
gtaagattggtgaaattcacaattccagacctaataaaattt---tattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgct-----acttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                  |  ||   | ||  |  || ||||   | || |||    ||| ||  ||| |    | |||| |   |  |   ||  | || |      |     ||||     ||||         || | |||  || | ||||    ||  ||   | ||  |  |||   ||| |  |  | ||   |  ||||||||||||||||||||||| ||||||||||| || |||||  | ||||| |||||||||||||||||| |||| || ||||||||||| | ||||   || 
----------------gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagttt---accttttcagtg--ctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                                   | |  |  |||  |  || | | || | ||     |      ||  ||  |||    | || | || |   | |  |    ||| ||||| ||  | | ||  | |||||||| ||||||||||||||||| || |||| | |||| ||||||||||| ||||| || ||||| ||| |||| ||    || ||  | |||
---------------------------------------------------------------------------------------------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatg-tagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatca-aatatatctgacagaacatttgtaac--taatttgtgactttttttttcctcttcttcttt-tcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                                           ||||  |  |   || |  | ||| |  |   || | ||   |     |||||  ||  | |||| ||| | |   |||  ||||  |      |||| | || ||||||||||| || |||||||| || |||| | |||| ||||||||||| || ||||| ||||| ||| |||| ||    || ||  | |||
-------------------------------------------------------------------------------------------------------tcgctttcgaattaagttgagtgaatttaggacgtgatgtgtccatcttg-tatttgcgacaatgatttttgattatgaattttttctttgtggacgccagACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttct-tcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                                                                                           ||||   | |  ||  |  |||   |  | || | | | ||| ||||||||| |||||||||||||| || ||||| || |||||| | || || ||||||||||||||||| ||||| || |  || || ||||| ||| | || 
----------------------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 14
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
                                                                                                                                                           ||||   | |  ||  |  |||   |  | || | |  ||| ||||||||| |||||||||||||| || ||||| || |||||| | || || ||||||||||||||||| |||||||| |  || || ||||| ||| | || 
----------------------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaacctttggtatttccatcacatcctttgttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATAAAAAACACCTACAATGGTTTTCGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
               aactaat  putative branch site (score: 2)
                 ctaatttgtgactttt  CT-rich tract
         atttgtaactaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA