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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

Basic information

species Vitis vinifera
transcript Vv11s0016g02550.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgt--atcattttatccataatgatggtgggacttgt-actctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                                   |   |  |  | |||||  || || |    || |||  ||  |   |    | |  ||     | | ||| | | | |||||   ||| | || ||| | ||||||||||||||||| |||||||| ||||| |||||||||||||| ||||||  ||| ||||||||||| || |||||
-----------------------------------gtgaagtttcgtaacctgaatgat-ggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
gtgcgattttcttc-ttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
  |  ||| | | | | || | ||  || ||| | |   |   | || | | |  | |||  |      | | ||| |  |   |   ||||    | | |||    ||||   ||  ||| | || ||||| |||||||||||||| || ||||| ||||||||||| ||||  || |||||||||   ||||| ||||||||||| |||||
--gtaattctgtacatgttaagatgaataatccatacttctt-tgaggatcatgaacaataaac-----tatttcactggagtaactctgattcatgta-ttgcttcctgaaactg--cagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                |   | | | ||| |  || | | || ||| | || |||| ||   |     |  || || |                   |  |||||||| || ||   ||||| || ||| ||||||| || || ||||| |||||||| |||||||||||||| ||||| ||||||   |  |||||||||||||||||  |
---------------gtgagactttgtcaaccgaatgactaaaaagaagcc-atatgatgact---gatacataatct-------------------agctgtactctaatttt---cagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatc----attttatccataatgatggtgggacttgtact--ctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                 | |  |||  ||| | |||   ||||||   |    | |   ||  | | |  || |    |||||  |   |   |   ||   | |||  |   ||    ||  ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||  ||||| ||||||    |||| ||||||||||| |||||
----------------gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttacttggaactg--cagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagca-acctatataattgatctaagtgtatcattttatccataatgatggtgggactt-gtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                                    |  ||||   |  | ||  |||||| |   |||      |||| ||  | ||   |  ||  | ||  |  | | |      |||| | || ||| |||| || ||||| ||||| || |||||||||||||| ||||| ||||| ||||||  ||| |||||||||||||| ||  |
------------------------------------gtgaaattctctcaactgaataattaaa--aaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
  |  ||||  | | | | ||    |  |  | | ||     |  |||   |  |||             |||  ||      | ||   || |     |  |||||  | ||    ||||| || ||||| ||||||||||| ||||| || ||||| |||||||||||||  ||||| ||||||    |||| ||||||||||| |||||
--gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagc--------acatatttttgctggaacaaacctgatccatgtgttactcaaaactg---cagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatcca-taatgat--ggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
           |||| ||   | ||   ||    |       | || |||      | || | |||    | |  ||  || || |||  ||   ||||  |||    ||||    ||  ||| | || ||||| || || |  || ||||| ||||||||||||||||| || || |||||||||||    || ||||| |||||||| || ||
-----------ttctgttatcagctgcaattgggattgtcggtgagaaac------agttaagctactaattttgttcaatacagtaacaattcagtggagctt----tctgtgtctg--cagCTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatc-taaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctg-atcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                  ||||  |  |||  |    ||||| |   |||    |||     ||  |||     || ||  |  | | |     |   | || || | |  | |||   ||| | || ||| | || || || || || || || |||||||||||||||||||| ||||| ||||| || || |||||||||||||| |||||
-----------------agaaaggtcacattgtcttagccaatt---caaatggtatcgac-attgaagatctgcagttggtgaacatttgct-taccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgcgattttcttcttttga-aatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
             |||   | ||| ||| | |||  |||  |||| |     ||   | || | |  |||||     ||| |  ||     | || | |    || ||   ||||   ||| | || ||| | ||||| || || || ||||| ||||||||||| |||||||| ||||| ||||| |  || || ||||||||||| |||||
------------gcttcaaataatgtat-agctagtggcttaatacgatgattagtcagtt-acccgagtgt-----tttctttattgaacttgtagaaac--tattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcat---ctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
     || || ||| | | |  | ||||      ||  |||    ||  |||  |    |  || |   | ||||  | | ||                 | ||||  | | ||| |   ||| | | |||||| || |||||||| || || || |||||||||||||||||||| ||||| ||||| |  || || || |||||||| |||||
-----atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatata-----------------agttgttttgt-atcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
          ||||  |  |||| ||    || |||||  || | |  |  ||  |  ||    |   ||| || |||     ||     |    | | ||    |  | | ||   ||| | || ||| | ||||| || ||||||||||| || ||||||||||||||| | ||||| ||||| |  || || ||||||||||| |||||
----------cttcaatcaaaatata---actgaaggcagaacaggggaattagttggtta---tgtttgtgtcgtttg---tattgaactcacagaaattac-ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
                                       ctctgat  putative branch site (score: 4)
         attttatccataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA