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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatctacctacctacattcattcattcattctctttttctagctgctatctccctccctcattaactttatgttttggtag

Basic information

species Vitis vinifera
transcript Vv04s0079g00600.t01
intron # 3
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 3
lower sequence: GLYMA11G33280.1 (Glycine max), 5'ss of exon 2
CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatctacctacctacattca--ttcattca-ttctctttttctagctgctat-ctccctccctcattaactttatgttttggtag----------
| || ||||||||||||||||||||||| || || ||||||||||| |||||||| |||| ||| ||||||||  | |   | || || |||  ||| ||||   | ||| ||| ||| | |  |  | | || | ||   | || ||  |   ||| | || | | |   ||  || |   | |  ||           
CTATTTGTGTTGCTGCTATCCTTGGTTCAACACTAAATGGAGAATTTGAAGATGTCAAACGCTTAAATGATCTCCTAATTGAAAAGAATAAAATAACTGGgtgtgtctctgccttcctccctctagctccctttacttaaatgttccttacatttatacaccatgcatgtctagattgaatatcttatatatattctata

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G40840.1 (Glycine max), 5'ss of exon 4
CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatc-tacctacctac--attcattcattcattctctttttctagctgctatctc--cctccctcattaactttatgttttggtag---------------------
|||| ||||||||||||||||||||||| || || |||||||| || |||||||| |||| ||| ||||||||  ||    | || || || ||||| ||||   |||   || ||   |   | || ||  | | | || ||||   | ||    | |         | ||| |   |  |  |||  |                      
CCATTTGTGTTGCTGCTATCCTTGGTTCCACTCTGAATGGAGAGTTTGAAGATGTCAAACTCTTAAATGATCTCCTGGTGGAAAAGAATAAGGAAACTGGgtttgtattgcacatattgattgagtctttactgcttcctattttgtgaactaaagtttaaggtattttaatttagacttggaattgacatgtgaaattaattattgggtag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G04940.1 (Glycine max), 5'ss of exon 4
CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatctacctacctacattcattcattcattctct----ttttctagctgctat-ctccctccct-cattaactttatgttttggtag--------
| || ||||||||||||||||||||||| || || |||||||| || |||||||| |||| ||| ||||||||  | |   | || ||||||  ||| ||||   | |||  ||  ||   ||   ||   |  |   |     || ||  ||  ||| | || ||| | | || | |  || | ||  |          
CTATTTGTGTTGCTGCTATCCTTGGTTCCACACTAAATGGAGAGTTTGAAGATGTCAAACGCTTAAATGATCTCCTAATTGAAAAGAACAAAATAACTGGgtgtgtctctttctttctttctttcctctccctctacttaaatgttccttacttttatacaccatccatgccttgattgaatatcttcatttaaatattc

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G39170.1 (Glycine max), 5'ss of exon 5
CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatctacctacctacattcattc---attcattctctttttct--agctgctatctccctccctcattaactttatgttttggtag--------------------
|||| ||||||||||||||||||||||| || || |||||||| || |||||||| ||||  || ||||||||  ||    | || || || ||||| ||||   ||| | |  |  |  ||| | ||   | |  |||   |||| |  | ||  | |      |  | ||| |   |  |  |||  |                     
CCATTTGTGTTGCTGCTATCCTTGGTTCCACTCTGAATGGAGAGTTTGAAGATGTCAAACTTTTAAATGATCTCCTGGTGGAAAAGAATAAGGAAACTGGgtttgtat-tgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtag

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|110732551|gb|EE107937.1|EE107937
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAGAACAAGGAACCGGG                         ATGGGGTACTCCAATCCATGT
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGT
EST: gi|46917851|gb|CN547180.1|CN547180
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|352764779|gb|FQ471839.1|FQ471839
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAAG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|30125561|gb|CB910900.1|CB910900
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|26262418|gb|CA813481.1|CA813481
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|34548841|gb|CF517073.1|CF517073
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|29785100|gb|CB341828.2|CB341828
EST:     TCTTTTGACAAAG-AAGATAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: TCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|30324791|gb|CD008053.1|CD008053
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|30129897|gb|CB915236.1|CB915236
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGNGATACTCCAATCCATGTAGATGCAGCAAGT
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGT
EST: gi|34545806|gb|CF514038.1|CF514038
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|110688418|gb|EE066946.1|EE066946
EST:     GATGTTAAACACTTGAATGATCCTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCC
EST: gi|110720857|gb|EE097156.1|EE097156
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|110697963|gb|EE075429.1|EE075429
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|32270055|gb|CD719214.1|CD719214
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
EST: gi|110712431|gb|EE090048.1|EE090048
EST:     GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGG                         ATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC
genomic: GATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatct ... gttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATCTGTGTTGCTGCTATCCTTGGTTCTACCCTCAATGGAGAATTCGAAGATGTTAAACACTTGAATGATCTTTTGACAAAGAAAAACAAAGAAACAGGgtacctatctacctacctacattcattcattcattctctttttctagctgctatctccctccctcattaactttatgttttggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA