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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG

Basic information

species Vitis vinifera
transcript Vv10s0003g05720.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagt-tctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
|||||  |||        | | | |  ||| |  |  | ||  |  |   ||  || |   ||    |   || ||||| | | | |  | ||  ||  |||| |||||||| ||||| ||||| || |||||||| ||||| || |||||||||||||||||||||||||| ||||| ||
gccacgttggcaagtgaatatgt-acatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatc--tcaggtattggatatattttg-agtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
    |  | ||  |   |      | | | ||   ||||  |    |     | |   || | ||| |||||| ||| |||  | || ||||      |  ||||||||||||||||||| || || || |||||||| || || |||||  |||||||||||||||||||||||||||| | 
--gtcgatagaaaattgtagaaaaaatggcatggtaatcatttgtttgccaaagagccttggcagtgtgttttttatgtatt-tactttcatgataattgcagGCTTATTCAACAGTTGGTACACCTGATTACATTGCTCCGGAGGTACTATTGAAGAAAGGATATGGAATGGAGTGTGACTT

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G049088_T02 (Zea mays), 3'ss of exon 5
gccactctggactacacttctt--ttatttgaataaaaatc---tcaggtattggat-atattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
  ||    | |   | |   ||  | || ||  ||||| ||    | |||  ||  | ||||  |        || || |  || ||||    ||    | | |||||||| || || ||||| || || || |||||||| || || ||||| ||||||||||||||||||||||| ||||| ||
--catatggaatggctcagattggtcatctgtttaaaactcatgcctggttctgtttcatatccttgactctattggtgtgcatggttc----atgaaatttatagGCTTACTCTACTGTTGGTACACCTGATTACATTGCACCCGAGGTACTCCTGAAGAAAGGATATGGAATGGAATGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 5
-gccactctggactacacttcttttatttgaataaaaatctcag-gtattg-gatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
 | |  ||  || | | |  |||||   | |       |||    |   || | || | || |||     ||   || | || |       | ||  |   |||| || |||||||| || || || || || ||||| |||||||| || ||||||||||||||||||| ||||||||| ||
tgtctatcaagattcc-ccccttttccataagcttccttcttgctgcgctgaggtacactt-gagcacagttgacatgtttaatcgcaattt-tgggacacagGCATACTCAACAGTCGGTACACCTGATTATATTGCTCCAGAAGTGCTACTGAAGAAAGGATATGGAACGGAGTGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
        | |||    |  |  | |  ||||| | | |            ||  ||||| |  |||  |  |  |     || | ||| || | |       |||||| ||| ||||| || |||||||| ||||||||||| || || |||||||||||||| ||||||||||||||||||||
tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataag-----atggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------gccactctggac-tacacttcttttatttgaataaa-aatctcaggtattggatat---attttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                                                                                            || |   |  ||   |     || | |||  ||| |  | ||  ||| ||   | |   |     ||||     |  | |  || |||     | ||||    |||| ||||||||||| || ||||| |||||||| || || ||||| ||| ||||||| || ||||| ||||||||||| ||
gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctgcgcgcgagaattcacgcgcgtacattctttttagatatatgacctgtggtttttatttttcgaccactagtcaaacatcaagtattaattccaggttttgctcatcagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttga--gtctgttttgt-atttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                                                                 | ||   ||  |  |   |||| ||| | |     |  | |||   |   ||||   |||||  | | |  ||| |        | |   ||  |||| ||||||||||| || ||||| || || ||||| || |||||||||||||||||||| ||||| ||||||||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgt-----tttgtatttatagttctgtcatatgctatc--tagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                                                                             | || |  |||| |   | ||  ||  ||  |    ||| |    ||| |  |   | ||| |     | |   |||   ||| || || | | | ||   |||| ||||| ||||| || ||||| ||||| || || || ||||||||| ||||||| || ||||| ||||||||||| ||
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatg--taggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtc-atatgctatcta---gGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                                                |    ||  |||    |  ||| | |    | || | || |  || | | ||   |||||||||||| || ||||| || || || ||||| || ||||| || |||||||| ||||| || ||||||||||||||
------------------------------------------------gtgcgtagcttgtacttccttt-tgtcccgatttttatctaagtgttctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG

upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                                        |     ||| |  |  |||    | | ||| ||| ||   |||  | |          ||||||||||||| || ||||| || || || ||||| || ||||| || |||||||| ||||| || ||||||||||||||
-------------------------------------gtgcgtagcttgtacttccttttgtcccgatttttatctaagtttcctttaa--------cagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
                     ttttgtatttatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
gccactc
- - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcat