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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag

Basic information

species Vitis vinifera
transcript Vv04s0008g02040.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os05g26890.1 (Oryza sativa), 5'ss of exon 9
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag
|||||||| ||||| |||||| | ||||| ||||||||||| ||||||||| |   ||| |||||  ||| |    | |  | |    |   | |   || ||     ||||||   |  || ||| |   |   | | | |   
AAAACATCATTCATTCTGTTTCTCAACAAATTTGATATATTCGAGAAGAAAATACAAAAGgtaaggcctgctctttgtacca-atgcatagtttagtactaaatg---ttaccaacatttatgttt-acgctggttacgtag---

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA04G05960.1 (Glycine max), 5'ss of exon 12
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag
||||||||||||||| | ||||||||||||||||| |||||||| ||||| ||  | || |||||| |     | |  |||| ||   ||  |||||  || |     ||| || ||  |   ||| |||  ||      || ||
AAAACATCCTTCATGTTATTTTTAAACAAGTTTGACATATTTGAAAAGAAGGTCCTGAATgtaagaaccatccagatgagtacac---tttgtcataggtggagtgtattatcatttcag---tttaataccttgcattgtgcag

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA14G11140.1 (Glycine max), 5'ss of exon 11
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag
||||||||||||||| | || |||||||||||||| ||||||||||||||  |  | ||||||||| |  ||   |    | ||||| |||  | | |  ||      | | || ||  |     | || | ||      || ||
AAAACATCCTTCATGTTATTCTTAAACAAGTTTGACATATTTGAGAAGAAGATCCTGAAAgtaagaacc-atctgaatgttgtacattttatccttgctggagcggtatcatcatttcagtctaataatgtcttgcattgtgcag

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA17G34450.1 (Glycine max), 5'ss of exon 11
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag
||||| ||||||||| | || |||||||||||||| ||||||||||||||  |  | ||||||||| |  ||   |    | ||||| |||  | |    || |   | |   | |||   |||   || | ||      || ||
AAAACGTCCTTCATGTTATTCTTAAACAAGTTTGACATATTTGAGAAGAAGATCCTGAAAgtaagaacc-atctgaatgttgtacattttatccttgttggataggttatcataatttcagtct--aatgtcttgcattgtgcag

upper sequence: Vv04s0008g02040.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT2G26300.1 (Arabidopsis thaliana), 5'ss of exon 12
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatct-tactcatacctgaaaaagtttaccagtt---tggatctttgatattttctgcattgtag
|||||||||||||||||||| || |||||||| || |||||||||||||||||| |  | ||||||    |  |||||| |||  || | |  | |||    |  |||| |    |||   |    ||||  ||||   ||     |||
AAAACATCCTTCATGCTGTTCTTGAACAAGTTCGACATATTTGAGAAGAAAGTTCTTGACgtaagaag-aactaaagca-tatttatttgttttgataggcaagcaagtctttttgttcaataacgctttcttattcaatgtgc-atag

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|351055432|gb|FQ442030.1|FQ442030
EST:     TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTCTAAAA                         GTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
genomic: TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctg ... tgcattgtagGTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
EST: gi|351046433|gb|FQ453049.1|FQ453049
EST:     TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTCTAAAA                         GTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
genomic: TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctg ... tgcattgtagGTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
EST: gi|33403897|gb|CF209524.1|CF209524
EST:     ATGTCGT-TTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTCTAAAA                         GTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
genomic: ATG-C-TGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctg ... tgcattgtagGTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
EST: gi|33403814|gb|CF209441.1|CF209441
EST:     TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTCTAAAA                         GTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA
genomic: TCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctg ... tgcattgtagGTGCCACTAAATGTATGTGAATGGTTCAAAGACTACCAACCAGTTTCAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACATCCTTCATGCTGTTTTTAAACAAGTTTGATATATTTGAGAAGAAAGTTATAAAAgtaagagctgataaaagcagtatacatcttactcatacctgaaaaagtttaccagtttggatctttgatattttctgcattgtag

- - - - - - ATGCTG
- - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - -  AAGAAA