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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAAATATGAATCTGAAGATGGGAAGAAGGATATTCAAGCTCAATTGGAGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggcactgacatatcctatatggaatggatttgtag

Basic information

species Vitis vinifera
transcript Vv12s0035g01020.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G61580.1 (Arabidopsis thaliana), 5'ss of exon 4
TAAGAAATATGAATCTGAAGATGGGAAGAAGGATATTCAAGCTCAATTGGAGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggcactgacatatcctatatggaatggatttgtag
||||||| ||||| ||||||| ||||| || |||||||||  |||||||||||| |||||||||||||||  ||| ||  | ||| | || || || ||||||   | ||||      || ||   ||||| |  | ||   || || ||||          ||| |  ||||         || || |  ||                  
TAAGAAACATGAAACTGAAGAAGGGAAAAAAGATATTCAAAGTCAATTGGAGAAGATGAAGAAGTACTGCTCTGTCATCAGAGTTCTTGCTCACACTCAGgta---tgccatt-----tacttcaaattcacaatcatt---ttgcaaattt-----catttgtttctgattacgattgttggatatgttttag-----------------
















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|351052229|gb|FQ452383.1|FQ452383
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|352791519|gb|FQ481098.1|FQ481098
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|349809727|gb|FQ398352.1|FQ398352
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351045493|gb|FQ440678.1|FQ440678
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351055977|gb|FQ453438.1|FQ453438
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351033284|gb|FQ446516.1|FQ446516
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351048267|gb|FQ442237.1|FQ442237
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCCGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351026538|gb|FQ432436.1|FQ432436
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|161714899|gb|FC064521.1|FC064521
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|349812497|gb|FQ407116.1|FQ407116
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351045744|gb|FQ440929.1|FQ440929
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|110687580|gb|EE065148.1|EE065148
EST:     TTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: TTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|349810715|gb|FQ402958.1|FQ402958
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351027369|gb|FQ444618.1|FQ444618
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|351048851|gb|FQ449719.1|FQ449719
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
EST: gi|352795550|gb|FQ480138.1|FQ480138
EST:     AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAG                         ATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT
genomic: AGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttcc ... ggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAAATATGAATCTGAAGATGGGAAGAAGGATATTCAAGCTCAATTGGAGAAAATGAAGAAGTACTGCAATGTGATTCGTGTTTTGGCCCATACCCAGgtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggcactgacatatcctatatggaatggatttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT