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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG

Basic information

species Vitis vinifera
transcript Vv11s0065g00640.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G469298_T01 (Zea mays), 3'ss of exon 5
gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
        ||    |  | |     |  ||||  |||    | ||   |  |||||| |  |    |||   |   |  |  |      || || || || | | |  | ||  |||| || ||  || |     | |||||||||||||| ||||||||||  ||||| ||||| |||| ||||||||| |||||  | ||||
------gtatagtatcctagag---acctagactttt---gtctatgaa--atgtaaatttc--acttgtcatgcataagcttataaactgcatatttttta-gATCCTTGATAATTGCCCTGGAGATTTGACCCAATGGTATCGCCACATATCAAAAGGTGGATGGCCATTTTCTACCGTTGATCATGGTTGGCCTGTATCAG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G341010_T01 (Zea mays), 3'ss of exon 9
gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
|| | | |||  |  | | | ||  |         || |  | |    ||  | | ||| |   ||   ||  || ||    |  | |         |||  || |  | ||  | || |  |   || |  |  | |||||||||||||| ||||||||||  ||||| ||||| || | ||||||||| |||    | ||||
gtacatacatgcc--agtagcatggagaccttgactttttgtctgtgaatggt-tgatttctt-gtggcatacttatcaacttcctat---------gttttagATCATTGACAACTGCCTCGAAGATTTGAACCAGTGGTATCGCCACATGTCAAAAGGTGGATGGCCATTTTCTACAGCTGATCATGGTTGGTGTGTATCAG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G00430.1 (Glycine max), 3'ss of exon 10
gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
                    |  || ||| | | ||   | ||||      ||  | || |||   |||||  |||| |  ||  | ||||     | |  |||||||||||||||||||||||  ||||| || | ||||| || |||||||||||||||||||||||||||||||| || |||||||||||||| || || |
--------------------gtgttcttttgcatttatcattttaagttgcattgacttgcccttgttgataattttttttct--tttttg-----tttaaaagGTTTTAGAAGATTGTCCAGGTGATCTTAATAAATGGTACCGTCACATTTCAAAAGGTGCTTGGCCTTTTTCAACTGGAGATCATGGATGGCCAATTTCTG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgctttcatcacttattgggatttatttagaactttc--taatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgt-----tgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
                          ||| | |    |  | | | | |   |  ||  | |    | |   |  |||||   ||  || |||  | || |     |  |||| |||||||| || || ||  ||||  |||| ||||||||||||||||| ||||| ||||||||||| ||||| |  ||||| || ||||||||||| |
-------------------------gtttgggataggcagttaatgaaaatcagcgtgttgctttggat--gttcttttccctctcatgattgtttcttttcatggtatagGTGTTAGAAGACTGCCCTGGAGATCTGAATTACTGGTATCGCCACATTTCTAAAGGGGCTTGGCCTTTCTCAACTGCAGATCACGGTTGGCCCATCTCTG

upper sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 9
gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaa--tgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
       | ||     |  | | ||  | |    ||  | | ||  |  | |    |||    ||| | |  |     |     |  ||| ||  |||   |||||||   |||||||| ||||||  || | |  || |||||||| || ||||| ||||||||||||||||||||  |  | || || |||||||| ||||| |
-----aacgtcgtgagtgtgtactttctaaatgtttgtttactt-taattcacaatatttgttagtattagttgcacttacagagattttaaacgtgtctctgaagGTGAGAGAAGATTCTCCAGGGGATATGGCCTACTGGTATCGTCATATTTCTAAAGGTGCTTGGCCTTTTTCTTCAAGAGACCACGGATGGCCTATCTCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71865816|gb|DT014871.1|DT014871
EST:     AATATGGTCCAACTCTAAGAAAAGCACATGCATACTTGAAGAAGTCACAG                         GTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA
genomic: AATATGGTCCAACTCTAAGAAAAGCACATGCATACTTGAAGAAGTCACAGgtgctttcat ... gttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA
EST: gi|161713441|gb|FC063719.1|FC063719
EST:     AATATGGTCCAACTCTAAGAAAAGCACATGCATACTTGAAGAAGTCACAG                         GTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA
genomic: AATATGGTCCAACTCTAAGAAAAGCACATGCATACTTGAAGAAGTCACAGgtgctttcat ... gttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA
EST: gi|161713540|gb|FC063135.1|FC063135
EST:     GCATACTTGAAGAAGTCACAG                         GTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA
genomic: GCATACTTGAAGAAGTCACAGgtgctttcat ... gttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG
               gtttgat  putative branch site (score: 5)
                    atcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttcatcacttattgggatttatttagaactttctaatttacagataatgtaattccccagtttgatctttttctggctggtgtttgaatgttgttgaagGTTTTAGAAGATTGTCCAGGCAATCTTGATTATTGGTATCGCCACATTTCAAAAGGTGCTTGGCCTTTTTCAACCGGTGATCATGGATGGCCCATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA