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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagccttacagtttctatcgttttgctttatttttgtggtcatcactctgcttttccttgctcag

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 10
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagc-----cttacag-----tttctatcgttttgcttta---tttttgtggtcatcactctgctttt-ccttgctcag------
||||| |||||||| |||||||||||||||||  || |||||||| ||||  ||||  ||||||||||||||||||||||||| || ||||||||||| || ||||| ||  ||  |      | ||       ||||||  |||       |   | ||| |  ||||   | | |||||    |   |        
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggt-tgctaattatatgacaccgattgacgaattgctttctaatgttcaataaaaaattatttatattcattggttttcttttatactatcctattatag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G01930.1 (Glycine max), 5'ss of exon 10
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagccttacagtttctatcgttttgctttatttttgtggtcatcactctgcttttcct--tgctcag-----------------------------
||||| |||||||| |||||||||||||||||  |  ||||||||||||   ||||  ||||||||||||||||||||||||| ||||| |||||||| || |||||||   || || | |        || | |||   || ||||  || |||  |      | ||| |  |  | |                              
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTGTTGTGGCTTCATTGATGAAGATTGCTAATGATATACGGTTATTGGGAAGgtaggt-tgctagtaatatggcatcaactaactaattgctttttctt-ttttaatgttcaatagaaaattattcataatatttaatgagtttgcgtaatgctatcctattatag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 10
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagc-----cttacagtttctatcgttttgctttatt--------tttgtggtcatcactctgcttttccttgctcag------
||||| |||||||| |||||||||||||||||  |  |||||||| ||||  ||||  ||||||||||||||||||| ||||| || ||||||||||| || ||||||||  ||  |      | ||   ||   |  |  || |  ||         ||| |  ||||   | | |||     |   |        
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCCCTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGACATACGGTTGTTAGGAAGgtaggt-tgctagttatatgacaccgattgacgaatttctttttcatgttcaatagaaaattatttatattcatgggttttcttaatactatcctattatag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagccttacagtttctatcgttttgctttatttttgtggtcatcactctgcttttccttgctcag
|||||||| ||||| | ||||||||| ||||| ||| |||||||  | || || || ||||||||||| || ||||||||||| ||  | |||||||||| || ||| |      |  |||   |||   |  |||  | |    | |||  | ||   |   | | || ||    ||
GCTGCACACGATGCTTGTGTTGAAACCAGTGGGTCACTTAACACAATCGCCACATCGCTGATGAAGATCGCCAATGATATACGTTTTCTTGGAAGgtatggat-ctaatctatagggattatttttttctttctttaacatgcactatgtccttatggtttaccatgtctttatatag

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|352794271|gb|FQ479513.1|FQ479513
EST:     GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
EST: gi|110363110|gb|EC926680.1|EC926680
EST:     GTTGCTACTTCCGTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
EST: gi|110407161|gb|EC972758.1|EC972758
EST:     CTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: CTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
EST: gi|110361036|gb|EC924487.1|EC924487
EST:     GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
EST: gi|110698892|gb|EE076910.1|EE076910
EST:     CCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: CCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
EST: gi|351045827|gb|FQ441012.1|FQ441012
EST:     GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAG                         TGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG
genomic: GTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgc ... ccttgctcagTGGTCCACGTTGTGGCCTTGGTGAACTCATTCTTCCTGAAAACGAGCCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagccttacagtttctatcgttttgctttatttttgtggtcatcactctgcttttccttgctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA