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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctcttaccccatttcctattcctactctatttcttccttgtccttttcttctgctatccaatctcagatgatttgattcttgtcagggattt...

Basic information

species Vitis vinifera
transcript Vv04s0079g00600.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G04940.1 (Glycine max), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctcttaccccattt-cctattcctactctatttcttccttgtccttttcttctgct-atccaatctcagatgatttgattcttgtcagggattt-
||| || |||||||| |||||||| ||||| || ||||||||  ||||||| |||||||| ||||| |||||||||||||||||||||||||||||||||||  ||  | ||  |   || |   |||   |||| | || |||| |  || | |  ||||  | ||   || |    |  |||  ||||||  | |      
GACGACTTGGATGGAGCCAGAGTGTGATAAACTCATCATGGCTGCCATTAATAAGAACTATGTTGACATGGACGAGTACCCTGTCACCACTGAGCTACAGgtaactaaccctaccaatatctatatatcgatactatcttccttcttcatcttctctttctctttattttatttt---ttttttccttcttggaatgttgcct

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G40840.1 (Glycine max), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctcttaccccatttcctattcctactctatttcttccttgtccttttcttctgctatccaatctcagatgatttgattcttgtcagggattt-----
||| || ||||||||||| ||||| || || || ||||||||  |||||||||| || ||||| || ||||| ||||||||||||||||||||||| ||||    |  | | ||  ||||  | |  |  || || |||  |    |||| ||   ||  |  ||   |  | | || ||   ||  | ||  | |  ||     
GACGACGTGGATGGAACCTGAGTGTGACAAACTCATCATGGCTGCCATTAACAAAAATTACGTCGACATGGATGAGTACCCTGTCACCACTGAGCTCCAGgcaagtatcacatataccata-cttgatattaatcaattattaa--tgtcgttcaattaagg-atgagagataacat-atactatattcgtaggagtattaattt

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G39170.1 (Glycine max), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG-
    || |||||||| || || || || || || ||||||||  |||||||||| |||||||| || ||||| ||||| |||||||||||||| || |||    || || | ||  | |   |||| | ||   |     ||    || | | |  |    ||||   || |  |   |||| |||| | | || |    |  |  
----ACGTGGATGGAGCCTGAATGTGACAAACTCATCATGGCTGCCATTAACAAAAACTACGTCGACATGGATGAGTATCCTGTCACCACTGAACTCCAGGCAAgtcccacactaattcattattttcaatcatcagagataaaattttcatttaatcaatttctcacatgcggtt--agataatttaaatattctttaagtgtga

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S34_308V6.1 (Physcomitrella patens), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctcttaccccatttcctattcctactctatttcttcc--ttgtccttttcttctgctatccaatctcagat-gatttgattcttgtcagggattt
||| ||||||||||| |||||||| || ||||| ||||||||  || | |||||||||||| |||| ||||||||||||||  | ||||||||||| ||||||    ||  ||||| | ||    |   | | |       || |   |||   |||||    ||   || |  ||  | || |  |||    ||   ||   
GACGACATGGATGGAGCCAGAGTGTGACAAGCTCATCATGGCGGCCCTCAACAAGAACTACATTGACATGGACGAGTACCCGATTACCACTGAGCTTCAGgttttagccctttacctc-ttcagaaactcaattgcggaggttacggctgtagatttctgtcactggtcattgccattttgagtgcattgcactctacgac--

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S68_116V6.1 (Physcomitrella patens), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctct-----taccccatttcctattcctactctatttcttccttgtccttttcttctgctatccaatctcaga-tg-atttgattcttgtcagggattt
||| ||||||||||| || ||||| |||||||| || ||| |  |  | |||||||||||| |||| ||||||||||||||  | ||||| ||||| ||||| |   ||| |     | | |  |  | |   | |     || | ||  | ||| || |  | |||  | ||  |  ||| || ||||  | ||||  |       
GACGACATGGATGGAGCCTGAGTGTGATAAGCTCATTATGTCTGCGCTCAACAAGAACTACATTGACATGGACGAGTACCCAATTACCACCGAGCTTCAGgtgcgagcctttagacatcctcggtaacgtggactttgagcatctgttgatcgtcgttatgct-tgcattgcaccccaagagtgtatttagtgcttgcgaa------

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ18071 (Selaginella moellendorffii), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcc-----------tccctcttaccccatttcctattcctactctattt-cttccttgtccttttcttctgctatccaatctcagatgatttgattcttgtcagg-----gattt----------------
 || || |||||||| || ||||| ||||||||  ||||||||||  | |||||||| ||| | |||||||||||||| || || ||||| ||||| |||||||            ||  ||   |   | ||   ||     |  | ||| |||  |||   |||  |     |    || | |    | |||  ||  | | |       | |||                
CACCACTTGGATGGAGCCCGAGTGTGATAAGCTCGTCATGGCCTCGCTCAACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaagaaaatatctttcgagcatgactttgcatgttcgcattgttttcttaattggtttttcgtgtgagtggagaaacgctagcgtttttttttctcttaaattaatggttttttgttttgctcgtag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ36644 (Selaginella moellendorffii), 5'ss of exon 2
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcc-----------tccctcttaccccatttcctattcctactctatttcttccttgtccttttcttctgctatccaatctcagatgatttgattcttgtcagggattt----------------
 || || |||||||| || ||||| || |||||  ||||||||||  | |||||||| ||| | |||||||||||||| || || ||||| ||||| |||||||            || |||   |   | ||   ||   | |  | ||| ||  ||     ||| |  ||  |  | | |     |  |||   |    | |  | |||                
CACCACTTGGATGGAGCCCGAGTGTGACAAGCTCGTCATGGCCTCGCTCAACAAGAATTACATCGATATGGACGAGTATCCGGTGACCACAGAGCTCCAGgttcgaaaagaaaatatctctcgagcatgactttgcatgtttgcattgtttttt--ttaatggtttttcgtgaaacgctagcgttttttttttctcttaaattaatggttttttgttttgctcgtag

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|110370088|gb|EC934268.1|EC934268
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|71858430|gb|DT007485.1|DT007485
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110732551|gb|EE107937.1|EE107937
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110719931|gb|EE095474.1|EE095474
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352764779|gb|FQ471839.1|FQ471839
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352777885|gb|FQ466938.1|FQ466938
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|71856790|gb|DT005845.1|DT005845
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110721944|gb|EE097740.1|EE097740
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110394088|gb|EC958547.1|EC958547
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|351014370|gb|FQ437372.1|FQ437372
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|34548841|gb|CF517073.1|CF517073
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|30129897|gb|CB915236.1|CB915236
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|34545806|gb|CF514038.1|CF514038
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352782597|gb|FQ476677.1|FQ476677
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110688418|gb|EE066946.1|EE066946
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|351022400|gb|FQ445175.1|FQ445175
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352795004|gb|FQ477114.1|FQ477114
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|351014363|gb|FQ437365.1|FQ437365
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|71858063|gb|DT007118.1|DT007118
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352785695|gb|FQ475698.1|FQ475698
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|349826582|gb|FQ418673.1|FQ418673
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|352794614|gb|FQ475112.1|FQ475112
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
EST: gi|110728467|gb|EE104071.1|EE104071
EST:     ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAG                         AATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG
genomic: ACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccct ... gtggatacagAATCGCTGCGTAAACATGATAGCACATCTATTTAATGCACCACTTGGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAACATGGATGGAACCAGAGTGCGATAAGCTAATCATGGCCTCCATTAACAAGAACTACGTTGATATGGACGAGTACCCTGTCACCACTGAGCTACAGgttcctccctcttaccccatttcctattcctactctatttcttccttgtccttttcttctgctatccaatctcagatgatttgattcttgtcagggattt

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctt