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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggagtcctttgtgttggagtggcttttgcttgtagtatgtattgattccattcctttgcaagaaattttggcagccttgaatctttaggttgagctggtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG

Basic information

species Vitis vinifera
transcript Vv19s0015g01160.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 9
gtaggagtcctttgtgttggagtggcttttgcttgtagtatgtattgattccattcctttgcaagaaattttggcagccttgaatctttaggttgagctggtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG
|||    | |||||| |          ||   |  |||||| ||    |  ||     |      |||| |    | | | ||||      ||  | ||  | |||         ||||||       || || |  | | || || || ||||||| || ||||||| |||  ||| ||||||||||||||||||||||||    ||||  ||||| | | | ||||| |   |||| || | ||| ||||||
gtaatgtttctttgtat-------atcttgtttcttagtatttacatgtgtcagcttct----gaaaatatatataacttggaattgccttgtcaaactattatat---------ggccaa-------ctaatgttggatatt-ctgatctgtagCTGGTACATAATGAGGAGGCAACATTTGTGAGGCAAATCACCAGAATGCCCAATGGTCAACATACATTTGACTCCT---TTCAAATGCACCCACTGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 9
gtaggagtcctttgtgttggagtggcttttgcttgtagtatgtattgattccattcctttgcaagaaattttggcagccttgaatctttaggttgagctggtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG------------------
                                |  | |||| | ||| |||      ||| || |     |  ||     ||||  | ||  |      |  ||  || |  ||  | | || | ||  |       |  | |||| || | ||||| || ||||||| |||  ||| ||||||||||||||||||||||||    ||||  ||||| | | | ||||| |||   || || | ||  ||||||                  
-----------------------------gtttcattgtatatcttgtttcttagtatttacatg---cctcagc--ttatgaaaatatacataacttggaattgccttgtcatatggccaactaatgtt-------ggatattctgatctttagctggtacataatgaggaggcaacatttgtgagGCAAATCACCAGAATGCCCAATGGTCAACATACATTTGACTCCTAT---CAAATTCCCCGACTGAAGGCAAGTATTGGTCTTCTT

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G48060.2 (Glycine max), 3'ss of exon 5
gtaggagtcctttgtgttggagtggcttttgcttgtagtatgtattgattccattcctttgcaagaaattttggcagccttgaatctttaggttgagctggtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG
                        |   |   |  | |||| | ||| |||      ||| || |     |  ||     ||||  | ||  |      |  ||  || |  ||  | | || | ||  |       |  | |||| || | ||||| || ||||||| |||  ||| ||||||||||||||||||||||||    ||||  ||||| | | | ||||| |||   || || | ||  ||||||
------------------------gtaatgtttcattgtatatcttgtttcttagtatttacatg---cctcagc--ttatgaaaatatacataacttggaattgccttgtcatatggccaactaatgtt-------ggatattctgatctttagCTGGTACATAATGAGGAGGCAACATTTGTGAGGCAAATCACCAGAATGCCCAATGGTCAACATACATTTGACTCCTAT---CAAATTCCCCGACTGAAG

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|110690338|gb|EE067360.1|EE067360
EST:     GGTGCCTGAAGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
EST: gi|30328313|gb|CD011575.1|CD011575
EST:     GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
EST: gi|32269703|gb|CD718862.1|CD718862
EST:     GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
EST: gi|32247565|gb|CD713384.1|CD713384
EST:     GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
EST: gi|32249844|gb|CD715663.1|CD715663
EST:     GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
EST: gi|32247747|gb|CD713566.1|CD713566
EST:     GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG                         CTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT
genomic: GGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAGgtaggagtcc ... taatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG
                                          ttctaat  putative branch site (score: 2)
                                      ttttttct  CT-rich tract
                               atttaagttttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggagtcctttgtgttggagtggcttttgcttgtagtatgtattgattccattcctttgcaagaaattttggcagccttgaatctttaggttgagctggtttatctggagattggccaaattgattctcatttaagttttttctaatttgtagCTTGTGCATAATGCGGAATCAATATTTGTGAGGCAAATCACCAGAATAGTTAATGACCAACAGAAACTCGACTCATATATTCAGATACGCCCTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG