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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA

Basic information

species Vitis vinifera
transcript Vv10s0003g04630.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g52940.1 (Oryza sativa), 3'ss of exon 2
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                            |  || | |||  |||||  |       |||| |  ||         | || || ||  ||        | | ||||||| | | |  |||||||| || ||||| ||||||||||||||||  |||||||| ||||||||||||||||||||||| || || |||||||| || ||    ||||| ||||
-----------------------------------------------------------gtgagtgc-ttacacttttagtgaccatgtgttgtgtaagg-------tatatttgtttgattcagcggtcatcttgctatttcttt--cagGTGGATACTATTTTAGACAAGGAAAATTTCAAGTTGGAGGACCTTCTTGATGAGGATGAAATAATCCAGGAGTGCAAAGCACTAAACACCCGCCTAATCA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                |  ||  | |      | ||||  |      | | |  ||| | |||| | | |  ||    |  ||| ||  |     |    ||||  || |      |||||||| || ||| | |||||||| || ||||| || || || |||||||| ||||||||||||||||| || |||||||| || |||   || || || |
------------------------------------------------tttttaacaaaa--aattcatttgggagacacaagtgaaat-tattagtatactatgggaacatctctacctaacccgcctaactttgtaatttactggtcagGTGGATACAATTCTAGACAAGGAGAACTTCACATTAGAAGAACTTCTTGACGAGGATGAAATAATTCAGGAGTGCAAAGCGCTGAATACTCGTCTCATAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G096107_T01 (Zea mays), 3'ss of exon 2
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                                     | ||   || |   | ||   |  |  |    |    |  |||    | ||  |||||     ||   | ||||| || |||||||| || |||||||||||||||||||| |  |||||||| |||||||||||||||||||||||||| || |||||||| || |||   ||| | ||||
--------------------------------------------------------------------gtgagtgcttgcagttcgatgttcatttattttttttctcctaagc--tacagttttttaaacattccttttatgtctttcagGTGGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAGGATCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G806347_T01 (Zea mays), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                              |  ||| | | |  |  ||    | ||       | | ||    | || ||  |  | ||||  ||| | ||    | |||| | | | |  ||  |   ||||| |            ||||||| || ||| ||||||| |||||||| || ||||| || |||||||||||||||||||| ||||| || |||||||| || ||     | || || |
----------------------------actgcaaatagcttgaaccatggaggcct-------ttcgtttttttcttcctcatttattgttaaagagaggt----tcttaactgtgctaacttagtgatttttttc------------agGTGGATACAATTCTGGACAAAGAAAATTTTACATTGGAAGAACTTCTTGATGAGGATGAAATTATTCAGGAGTGCAAAGCACTGAACTCAAGACTCATAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G000039_T01 (Zea mays), 3'ss of exon 2
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                            |  || | |  |  |   | | |  |  |    |   || || |  ||   |||  |  |     | | | ||| | ||| | | |  ||||| || || |||||||||||||||||||| |  |||||    |||||||||||||||||||||||||| || |||||||| || |||   ||| | ||||
-----------------------------------------------------------gtgagtgcttgcacttcgatgttcatgttttccctcctaaggtacaatt---atttgttaac----tgcacatttcgttatctcttt--cagGTTGATACTATTTTGGACAAGGAAAATTTTAAGTTGGAATGTCTTCTTGATGAGGATGAAATAATTCAGGAGTGCAAAGCACTGAATACCCGCTTAATCA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                           |  |||  ||     ||   |  |    |      ||  || ||         | | || |||   |      |  ||  | ||  |||  |||| ||| | || |||||||| || ||| | ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||| || |||||||| |||||    || || || |
----------------------------------------gggggcaatattttcggggccctgggcggcca-----ctcggctcgacccccc---acaggtacggccctg---tcttaattctgttaacttagtgctttattttttccagGTGGATACAATTCTTGACAAAGAAAATTTTACATTGGAAGAACTTCTTGACGAGGATGAAATTATTCAGGAGTGCAAAGCACTTAACTCACGACTCATAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatat-gtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                     | ||||  | |   | |    |||   |  || |||| | |  | |   |     ||  |    | || ||  |   | |||| | |||  | ||||||||||| || |||||||| ||||| ||||| |||||||| || || ||||||||||||||||| ||||| |||||||||||||||||  | |||||||| |
-------------------------------------------------gggggactagaataggttagtttaatttaatttttaaaatgatatgtagatacgta---ttggtatagcgattttactgtttatttggtgtattatattgcagGTGGAAACCATTTTGGATAAGGAGAATTTTACTTTGGATGAACTACTTGATGAGGATGAAATTATTCAGGAATGCAAAGCTCTTAACAGTCGCCTTATAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgtt-gcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                  ||  | |   |||| || |||  | | |||||| | | | |  | |     |||| ||   | ||||   |  |||       || | |  | |||| |||||| ||  | |||||||| || || | |||||| || ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || ||  | |
--------------------------------------------------ataatatg--ttgggacgttattcatattctacaatattttgctggctgcttgcgattcatagtcttatgtgctttctggaaatttcgaattttgtttgcagGTTGAAGCAATTTTGGATAAAGATAGTTTCACATTAGAGGATCTTCTTGACGAGGATGAAATTATTCAAGAATGCAAAGCCCTGAATGGACGACTCTTAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S112_230V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttcca-tatttttccc---tttttgctatatgtgt-tgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                                          ||  | | || |    | ||| |        | |||    |   |   ||   ||| |     ||||  | |    |  | ||| | |   | ||||||| ||| || |  | ||||| ||    | |||  |||| ||||| || |||||||||||||| || || |||||||||||||||||| | ||||| ||||
--------------------------------------------------------ctgcacgctgcagttgaatatttgtgtatattcgctttgctgataggtcattgatattttcttgctattagtgctaagtagtggctgtctacttatgcagGTTGAGTCGGTGCTCGACAAAGATGTCTACACCCTGGAAGAGCTCCTGGATGAGGATGAAATCATCCAGGAATGCAAAGCTCTTAATAGCCGCCTCATCA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S391_39V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
                                          |   |||    |     ||||||   ||    | |   | |  | ||||||| | | |||    | ||  |  |     ||| |  || |  |    |||      ||||| ||  || |  |||| |||||    | ||||||||| ||||| || ||||| |||||||| |||||||| ||||||||||||||| | ||        
------------------------------------------atgcaataggggc---acttggtttgttct-ttgtcgttgcgtgcatgtttttgcacagttgattgttgctgttaatgaattgtggccgtggtcacgtata-----cagGTTGACTCGGTGCTGGATAAGGATGTCTACACTTTGGAAGAGCTCCTGGATGAAGATGAAATCATTCAAGAGTGCAAAGCTCTTAATAGCCG--------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA
          ttttaat  putative branch site (score: 3)
          ttttaattcttccata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattccgtgtaccaaaaagaattacttataaaaaacatagataatcattgtctagcttggtacattaagctttttctactagaatgttttagaaaagtgcggttttaattcttccatatttttccctttttgctatatgtgttgcagGTGGAGACGATTTTGGACAAGGAAAATTTCACTTTGGAGGAGCTTCTTGATGAGGATGAAATAATTCAAGAATGCAAAGCTCTTAATGGGCGCCTTATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG