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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgaaattgactaattgcacattctccaaaaacttcgccggaagttggaaggaaggatgaatcacgtggagtttgacattttctttggttggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAGATTTTGTTAAGGTTGCCACTGGGAAGATGAATCCCCAAATTGCTTTTAT

Basic information

species Vitis vinifera
transcript Vv18s0001g10520.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g10520.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G36080.1 (Glycine max), 3'ss of exon 2
tcgaaattgactaattgcacattctccaaa-aacttcgccggaagttggaaggaaggatgaatcacgtgga-gtttgacattttctttggttggta---atctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAGATTTTGTTAAGGTTGCCACTGGGAAGATGAATCCCCAAATTGCTTTTAT-
      ||   | |||  ||    |      || ||    |     |   |  | |      |  |||| | |  | |   ||  || |||| |||   || ||||| | || |||||||| |||||||||||  | ||||| || |||||||| || |||||||||||||||   |||||||||||||| || |||||||| || 
------ttccatgattctactcaatttggccaattttattgtgttctctgacaatgctatcgtgtcgtgtatgagtaatgattatttgggtttgtatgtatttaggGTCATATGAAGGAGGAAAGCCTGATGCATCTTTTTCGTTTAAGGATGAGGACTTTGTTAAGGTTGCCTTAGGGAAGATGAATCCGCAGATTGCTTTCATG

upper sequence: Vv18s0001g10520.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G09100.1 (Glycine max), 3'ss of exon 2
tcgaaattgactaattgcac---attctccaaaaacttcgccggaagttggaaggaaggatgaatcacgtg-gagtttgacattttctttggttggta---atctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAGATTTTGTTAAGGTTGCCACTGGGAAGATGAATCCCCAAATTGCTTTTAT
      ||   | |||  ||   ||| | | |||  |     |     ||  |  |    || |||| ||  |||| |||  || | || |||| |||   || ||||||| || |||||||| |||||||||||  | ||||| || ||||| || || |||||||||||||||   |||||||||||||| || |||||||| ||
-----tttccatgattctacttaattttgccaaatttatcatgttctctgacaatactattgtatcatgtatgagtatga--ttattttgggtttgtatgtatttagGGCCATATGAAGGAGGAAAGCCTGATGCATCTTTTTCATTTAAGGACGAGGACTTTGTTAAGGTTGCCTTGGGGAAGATGAATCCACAGATTGCTTTCAT
















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|110692307|gb|EE071401.1|EE071401
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110731553|gb|EE106064.1|EE106064
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|30137388|gb|CB922726.1|CB922726
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110702006|gb|EE080226.1|EE080226
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|30128318|gb|CB913657.1|CB913657
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110406594|gb|EC972173.1|EC972173
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110428740|gb|EC995219.1|EC995219
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|71871632|gb|DT020687.1|DT020687
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|351025342|gb|FQ434355.1|FQ434355
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110730854|gb|EE108410.1|EE108410
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110401310|gb|EC967917.1|EC967917
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|30125163|gb|CB910502.1|CB910502
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110377019|gb|EC942080.1|EC942080
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110421606|gb|EC987905.1|EC987905
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110422438|gb|EC988763.1|EC988763
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110373216|gb|EC937434.1|EC937434
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110424832|gb|EC991205.1|EC991205
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|30133262|gb|CB918601.1|CB918601
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110380104|gb|EC945346.1|EC945346
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|34319348|gb|CF372102.1|CF372102
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
EST: gi|110429212|gb|EC995701.1|EC995701
EST:     CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAG                         GGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG
genomic: CAACGAGGAAATATACATTGTTGATCTCAAGAAAGGGGAAGTTACCAAAGgttagggtct ... ggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaggaaggatgaatcacgtggagtttgacattttctttggttggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAGATTTTGTTAAGGTTGCCACTGGGAAGATGAATCCCCAAATTGCTTTTAT
                         gtttgac  putative branch site (score: 4)
                                attttcttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgaaattgactaattgcacattctccaaaaacttcgccggaagttggaaggaaggatgaatcacgtggagtttgacattttctttggttggtaatctagGGCCGTACGAAGGAGGGAAGCCTGATGCCACCTTTTCTTTCAAGGATGAAGATTTTGTTAAGGTTGCCACTGGGAAGATGAATCCCCAAATTGCTTTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -aaattga
- - - - - - - - - -cattctc
- - - - - - - - - - - - - caaaaac
- - - - - - - - - - - - - - - - - - - - - - - -gaaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgtgg