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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGATATCAATCTCATTGAAGCAGCCATCAGAGATCCAAGAGGGGAGCTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggacccttcttttataaaactatcaccacatcattcatgacatgactttatgttttggtagattcccacattctggatgattcttccggcaaactg...

Basic information

species Vitis vinifera
transcript Vv14s0036g00520.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G41120.1 (Glycine max), 5'ss of exon 2
CTATGGATATCAATCTCATTGAAGCAGCCATCAGAGATCCAAGAGGGGAGCTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaag-gacccttcttttataaaactatc--accacatcattcatgacatgactttatgttttggtagattcccacattctggatgattcttccggcaaactg---
| ||||| ||  || | ||||| || ||||||||||||||||  |||||||| || || ||||||||||||||||| |||||||| || || ||||  |||||||  |   | || ||  |||| | ||  |  |   |||| ||    | | | |   || |   ||        ||  | | |  || ||    |  | ||   
CCATGGACATTCATTTGATTGAGGCTGCCATCAGAGATCCAAAGGGGGAGCTAGTATATCCAACCACAAGGCTTATTTGCTTGGAAAATACTCATGGAAAgtaagcaattatgctgttcaaaaattttctaaatagtacattaattggttaaatatcctttatataagcagtaagaatgattggtatttttttttcctgattgtag
















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|161719590|gb|FC069398.1|FC069398
EST:     CTTGTGTACCCAACCACTAGGCTTATCTGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
EST: gi|30300481|gb|CB977275.1|CB977275
EST:     CTTGTGTACCCAACCACTAGGCTTATCTGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
EST: gi|110362584|gb|EC926127.1|EC926127
EST:     CTTGTGTACCCAACCACTAGGCTTATCTGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
EST: gi|29785385|gb|CB342317.2|CB342317
EST:     CTTGTGTACCCAACCACTAGGCTTATCTGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGACGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTT
EST: gi|351043016|gb|FQ443858.1|FQ443858
EST:     TGTGTACCCCACCCACA-GGCTTATATGCTTGGAGAACACGCATGTCCA-                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATA
genomic: TGTGTACCCAACC-ACAAGGCTTATATGCTTGGAGAACACGCATG-CCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATA
EST: gi|161718610|gb|FC068205.1|FC068205
EST:     CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGT
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGT
EST: gi|161714104|gb|FC064393.1|FC064393
EST:     CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAA                         CTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAG
genomic: CTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggaccc ... ttgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGATATCAATCTCATTGAAGCAGCCATCAGAGATCCAAGAGGGGAGCTTGTGTACCCAACCACAAGGCTTATATGCTTGGAGAACACGCATGCCAAgtaaggacccttcttttataaaactatcaccacatcattcatgacatgactttatgttttggtagattcccacattctggatgattcttccggcaaactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcaaac