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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaatagctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA

Basic information

species Vitis vinifera
transcript Vv13s0073g00610.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 5
ccttgtgactaaggtttcttttatttctgagaaatcaaacacgt-gtgtgtgcctttgtctgttaatagctttgataaactgttccactggtggcca--acagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
      |||||   | | |  ||| ||||     ||||| || |     ||     |  | |||   ||||| |     ||| |    ||     |    ||||| |||||||||||||| |||||||||||||||||| | ||||||||  |||| ||||||||  | |||||||| ||||| ||| |  | || |||||  
--agccgactagcctctttaatatctctgctgt-tcaaatactttaaaggtttacgttccggttctgagcttgggatttctgctattatgcctatctgtgcagATTAATGACCGCTATGAATTCCCTTTGCAACTTGATTTGGATAGAGATGATGGAAAATATCTTGCTCCAGATGCAGATAGAAGTATAAGAAACCTTTATG

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 9
--ccttgtgactaaggtttcttttatt-tctgagaaatcaaacacgtgtgtgtgcctttgtctgtta-atagctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
      || | ||| ||    | |||  ||| |    ||| | |  |   | ||      || |  | | | | |||||  | |      |   |   |  ||||| |||||||| |||||||||||  | |||||||||||||| |||||  |||| ||||||||  | || ||||| ||||| ||  || | || |||||||
aattaagtaattaacgtgatatctatcctcttatttctcatata-ataattatggaaagttcagcaacaaatcgttgattgattaacgtccaatt---ctgcagATTAATGACCGGTATGAGTTCCCACTTCAACTTGATCTTGACAGAGATGATGGGAAATATCTTGCTCCTGATGCAGATAGAAGCATTAGAAACCTTTACA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 9
ccttgtgactaag-gtttcttttatttctgaga-aatcaaacacgtg--tgtgtgc-ctttgtctgttaatagctttgataaactgttccactggtggcca-acagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
      |   ||  || ||||||| || ||||  || ||  ||      | | | | |    | | ||  |    | | ||||||   | | |   | | |   ||||||||||||||||||||||||| || ||| | |||||||| |  ||  |||| ||||| || || ||||| || || ||||| || || || || || |
------gctcaactgtatcttttacttttgagggaaacatgcaaaatactttatacacacaattttttcctgcactggttaaactaaactaatttggacaatgtagATAAATGACCGCTATGAGTTCCCATTACAATTAGATCTTGACAAGGATGATGGAAAATACCTCTCTCCAGAAGCTGACAGGAGGGTGCGTAACCTCTATA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 9
ccttgtgactaaggtttcttttatt-tctgagaaatcaaacacgtgtgtgtgcctt------tgtctgttaa---tagctttgataaac--tgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
  ||   ||   | |   |   |   ||  |   || || ||| |   |    |||      ||     |||   || |   |||      || ||   |      |  ||||| ||||||||||||||||||||| | |||||||||||||||||||| ||||| ||||||||||| |||||||| ||| | ||| || | || || || |
-gttagaaccgtgctgaataccaccatccaaatgataaaccacttccatacatcttaagaaatggtgaataaggttacccaggattggtgatgatcttatctacttctgcagATTAATGACCGCTATGAGTTCCCTCTTCAACTTGATCTTGATAGAGACAATGGAAAATATCTATCTCCAGATGCAGATCGAAGTATTAGAAACCTCTATA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaatagctttgataaactgttccactggtggccaa-----cagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
                                                            |   ||| | |  | |    || ||   |  |||| ||  |   | | |        || ||  |   | ||||   |   || | |  |           ||||| ||||| ||||||||||||||| ||||||||||||| ||||||||   |||||||||  |  | ||| |||| ||| | |||   || || |||||||
gtttgttctgataacttgcacttcgttcagttagttatattgttcatgtactttagggtacacttgattgatttgtgcagtaattacaatcaatctaaatcaaatatattttaacacctattctttattgtgattgtcatgtctattaatacttgcttgcccagATTAATGATCGCTATGAGTTCCCTCTGCAACTTGATCTGGATAGAGATGGTGGCAAATACATTGCTCCAAATGCAGATCGAAGTACACGAAACCTTTACA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 5
ccttgtgactaaggtttcttttatttctgagaaat------caaacacgtgtgtgtgcct---ttgtctgttaatagctttga---taaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
            | | ||  |    ||||||| ||       ||| || ||| | || ||   |||  |  |     |||  |   |||| ||||    |  ||      ||||||||||||| |||||||||||  | ||| | ||||||||||||||  |||| |||||||| || ||||| || ||||| ||||| || || || || |
-----------ggatatcactatcatctgagacatgcattcaaaatacttgtctatggctgatttgcattcttgcgtcttctaaattaaattgtttttttt-tgtgatgtagATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTTCTCCAGACGCGGATAGAAGTGTGCGTAACCTATATA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 5
ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaata-----gctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
  || ||| |||  ||| | ||  ||   |  | || |       | | | | |||   | || | |       || | |   |  ||    || | | || ||||| |||||||||||||||||||| |||||||| ||||||||||  || ||||| ||||||||||| || || || || || ||| |||||||| |||| |
--ttatga-taatttttttcttggttt--attattccatttgtaatattttcttttactttttgacacatctatttggcttggccattaacttgattggcatcagATCAATGACCGCTATGAGTTCCCCTTGCAACTAGATCTTGATATGGATAATGGGAAATATCTATCTCCTGACGCAGACAGAAGTATTCGCAATTTTTATA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------ccttgtgactaaggtttcttttatttc--tgagaaat---caaacacgtgtgtgtgcctttgtctgttaatagct--ttgataa--actgttccactggtggcca-----------------------acagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
                                                        |||    |  ||   | ||||||   |||   |           |||||||||  ||||  |  |  | | |  ||| ||   ||| ||  |||  ||   |                        ||||| ||||| ||||||||||| ||| ||||||| || || |||||||||||||| |||||||| || || ||||| ||  | ||||| || ||| | ||||
gtgaggaaaggggttttcgaaccatgcaatatgcaacattcggctggtatagcttatgtattgattgtgcatattatttagatgaaggacgtgtgtgtgtgtgtgtgtgtatttgctttgttttggttggttggtagtcacttttttactactgattacctttgaacattatttatgtgatgcagATTAATGATCGCTATGAGTTTCCTCTGCAACTAGACCTGGATAGAGAGAATGGAAAATATCTCTCTCCTGATGCTGACCGCAGTGTGCGAAATTTATACA

upper sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 7
ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaatagctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
  |  |  ||     | | ||   |  ||    ||    |     |   |  |  ||  | |     | |||  | ||| || ||       ||   |||||||| || ||||| ||||| ||| ||||| | ||| | ||||| ||||| ||||||||| |||| || |||||||||||  | ||  | ||| | ||| 
-gtaatagcttgaactacgtt--gtgttggtggatggttcctagttccat-tcactgaatttgggctg-tttattgaacagtgcctaattatgctggcagATAAACGATCGCTACGAGTTTCCTCTGCAATTGGATTTAGATAGGGAGAACGGCAAATATTTATCGCCGGATGCCGATAGAGGCGTGAGGAATTTGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgcctttgtctgttaatagctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA
                        tttgataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgtgactaaggtttcttttatttctgagaaatcaaacacgtgtgtgtgcctttgtctgttaatagctttgataaactgttccactggtggccaacagATAAATGACCGCTATGAGTTCCCTTTGCAACTTGATCTTGATAGAGAGAATGGCAAATATCTATCACCAGATGCCGATAGGAGTGTTCGCAATCTTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
ccttgtg
- - - - - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccactg