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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatataaaagatatagtgtgttttttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgtggtggataatttttaatttctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC

Basic information

species Vitis vinifera
transcript Vv05s0029g01210.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
taatataaaagatatagtgtgttttttattaaaaaaaaaaaaacatgattgtt--taccattgcaatctaa--tgtggtggataatttttaatttctt--tttca----gGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
         | || ||||   ||  ||  |  | | ||     ||  ||||||  ||  |||    |||||  |  ||   | || | |   ||||||  |||||    ||||||| || |||||||| || |||||||| ||||| || || |||||||| ||||| ||  ||||||| || ||||| ||||  |||||||||||||| 
---------atatgtagttgtttgattgatgcatagaacttttca-aattgttattagtattctggtctaaatttcggattaaaactctcggtttcttgatttcaatcagGCAACAACAGAGTGATGAGACCCCAATGGTGTGGGAGATACTTCTATACATGTACATCCTTTACTCACCAGATTGGCATTACCGAAGTACAATGCCCACT

upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S70_225V6.3 (Physcomitrella patens), 3'ss of exon 2
taatataaaagatatagtgtgttttttattaaaaaaaaaaaa---acatgattgtt-taccattgcaatctaa-tgtg---gtggataatttttaatttctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
   |||  |  ||  ||   |||   ||||  |     ||     |   |||| ||  ||  |||  || |   ||||   |||   || ||||||         ||| ||||||||||| ||||| ||||| |||||||||| |||||| || ||||||||  | ||  |||| || || ||||| || |  |||||||||||||| 
---tattgatcatgcagcaagttacatattgtatttggaagttctatgagattcttacacacttgtcatttggctgtgcatgtgaccaacttttaa-----cgagcagTCAACAGCAAAGCGATGAGACGCCTATGGTATGGGCAATGCTTCTTTACATCTATGTACTTTACTCTCCCGATTGGCATTATCGCAGTACAATGCCCACT

upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S452_16V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------taatataaaagatatagtgtgtt---tt-----ttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgtggtggataatttttaatttcttttt--cagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
                                                                           |     | |||   || ||| ||   ||     |||||  ||    | |   | ||  || |  | |  | |  |  | |  ||  |   | |     ||||     ||| ||||||||||||||||| || || ||||||||||  ||||| || ||||||||| | ||| |||| || || ||||| || | |||||||||||| || 
gtaagatcttacatcttgctgtttagcagtttttaaccctctactactcgtccataaacgtcgatcttgtgaatctggataagaagggctaatgtcttggcttcaaaattatttcaatgtcacacttacgagcgtattgcctgaccagttcctttattgtttgcatgtgcgactcttgcgagcagTCAACAGCAAAGTGATGAGACTCCTATGGTATGGGTGATGCTTCTCTACATCTACGTGCTCTACTCTCCAGATTGGCATTATCGGAGTACAATGCCTACT

upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S55_117V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------taatataaaag---atatagtgtgttttttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgt---ggtggataatttttaatttctt--------ttt-----cagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
                                                                |||| |  |     |||| |  | |   |  ||  |   || |         | | |||| |     | || |||     | | || |||||  || | |        |||     ||| |||||||| |||||||| || || ||||||||||  ||||| || ||||||||| | ||  | || || ||||||||||| | ||| ||||||||||| 
gtaagctttttacactttacttttaacagtgctcatatacatcttactcgtccatgcctgtgcttaatgtggacatgcatatcgaatatcgatgttttgactgaatatttggaagatatataccctcaagttgtagtgtcttactagttactttttttttgcatgcgcgacgtttgcgagcagTCAACAGCAGAGTGATGAGACTCCTATGGTATGGGTGATGCTTCTCTACATCTACGTGCTTTATTCTCCAGACTGGCACTATCGGAGCACAATGCCCACA

upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ18347 (Selaginella moellendorffii), 3'ss of exon 1
taatataaaagatatagtgtgttttttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgtggtggataatttttaatttcttttt---cagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
| ||          ||       || || |   |  |       | || | |||    ||   ||||| | || |  |   |    || || ||||    |||||||||||| || || || || |||||||| ||||  |||||||| ||||||||| | ||| |||| ||||||||||||||||  || |||||||| || 
ttatcagttcttcctaagccaagttctactcctacgatctc--taggactttttggttttcagatcta-tatgttctaagttccaaaactttttttcttccagGCAACAGCAGAGCGACGAGACTCCAATGGTCTGGGTGATGCTCCTCTACATCTACGTGCTCTACTCCCCGGACTGGCACTACCGCAGCACAATGCCGACG

upper sequence: Vv05s0029g01210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ22064 (Selaginella moellendorffii), 3'ss of exon 1
-taata-taaaagatatagtgtgttttttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgtggtggataatttttaatttctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
 ||  | |      ||      ||| |      |  |     ||   |  ||| ||  ||   | || |  | |       ||   ||  ||||| || |||||||||||| || || || || |||||||| ||||  |||||||| ||||||||| | ||| |||| ||||||||||||||||  || || ||||| || 
ttatcagttcttcctaagccaagttctactcctacgatctctaagactttttggttttcagatctatatgttctaagttccaaaactt--tttctcttccagGCAACAGCAGAGCGACGAGACTCCAATGGTCTGGGTGATGCTCCTCTACATCTACGTGCTCTACTCCCCGGACTGGCACTACCGCAGCACGATGCCGACG

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|30133704|gb|CB919043.1|CB919043
EST:     ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCT                         GCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT
genomic: ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCTgtgagtacta ... tctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT
EST: gi|110710061|gb|EE086067.1|EE086067
EST:     ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCT                         GCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT
genomic: ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCTgtgagtacta ... tctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT
EST: gi|30128410|gb|CB913749.1|CB913749
EST:     ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCT                         GCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT
genomic: ATCATACTTGCCATTGGAAGCATCTTGCACCATTCATCCCTGCAACGCCTgtgagtacta ... tctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgtttaccattgcaatctaatgtggtggataatttttaatttctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC
                                     ttttaat  putative branch site (score: 3)
                                    tttttaatttcttttt  CT-rich tract
                                ataatttttaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatataaaagatatagtgtgttttttattaaaaaaaaaaaaacatgattgtttaccattgcaatctaatgtggtggataatttttaatttctttttcagGCAACAGCAAAGTGATGAAACGCCAATGGTATGGGAAATGCTCCTATACATCTACATTCTCCACTCACCGGACTGGCACTACCAGAGTACAATGCCCACC

- - - aaaagat
- - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggtgg