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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagcgtaaagattcctcaaccatgtgttaatcttctttctttccaagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC

Basic information

species Vitis vinifera
transcript Vv02s0012g01410.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G33780.1 (Glycine max), 3'ss of exon 1
agaagcgtaa-----agattcctcaaccatgtgttaatcttctttctttccaagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC
| ||   |||     | |||| | |||||| | |||   |||  | | |  ||  ||  |||| | |  | ||   |   |||     ||   | |  ||||||||| || ||||| |||||||||||  |||| | |||||| ||||||||||| | |||||||||||| |||||  ||||||||||||| |||||||||||||
acaaagttaatagctatattcttaaaccatttatta---ttcaatttgttaaaaaat--ttcaccatagttttcactaattttcttgctttgatatcatttacagTCAGGGTGCTGCAAGCCACCAACGCAATGTGCGTACACGTTTGTGAATCCAACCTATTGGATTAGTCCCATCAACACAGCAGCGGATATGGATTGCCTGC

upper sequence: Vv02s0012g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G02170.1 (Glycine max), 3'ss of exon 3
-agaagcgtaaagattcctcaaccatgtgttaatcttctttctttccaagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC----
    |      | |||| | | |||| | ||   |||| || | |   | | |  |||| ||| || ||   | | |||     ||   | |  ||| ||||| || ||||| |||||||||||  |||| | |||||| ||||||||||| | ||||||||||||||||||  |||| ||||| || |||||||||||||    
agttaatagctatattcttaagccatttttt---cttcattttatt--aatttttttcaccttaattttcactatttttcttgctttgatatcatttccagtcagGGTGCTGCAAGCCACCAACGCAATGTGCGTACACGTTTGTGAATCCAACCTATTGGATTAGCCCCATCAACACTGCAGCAGATATGGATTGCCTGCAATG

upper sequence: Vv02s0012g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G36610.1 (Glycine max), 3'ss of exon 2
---agaagcgtaaagattcctcaaccatgtgttaatcttctttctttccaagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC
     ||   |||| |      ||  |     |||     |   |   ||  |    ||  || || | | ||| ||| |||   ||| || ||    | ||||| |||||||| |||||||||||  |||| || ||||| |||||||| || |  |||||||||||||| ||  |||||||||  |||||||||||| || 
aatcaaattttaaaaaaaa---aattagagactaaaaacttagttaatcattttcttttattccttttgtcttaattcctttttattttttcttctgatgcagTCAGGATGCTGCAAGCCACCAACAAAATGTGGTTACACATTTGTGAACCCAACGTATTGGATTAGCCCTATCAACACAGCAGAAGACATGGATTGCATGA

upper sequence: Vv02s0012g01410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G11130.1 (Glycine max), 3'ss of exon 1
agaagcgtaaagattcctcaaccatgtgttaatctt-ctttctttccaagtatggttcatc-tttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC
  |        ||||| ||||||| ||||||  ||| | || ||| |    ||    | |  || |||||||   | | || ||||| ||  |    | ||||| || ||||| |||||||||||  |||| || ||||| ||||||||||| |  |||||||||||||| ||  |||| ||||  |||||||||||| || 
--attaaccgggattcttcaaccacgtgttatcctttcattttttgcccccattacacgttattcatctttttcctttattcctttttttcatctcatgcagTCAGGGTGCTGCAAGCCACCAACAAAATGTGGTTACACGTTTGTGAATCCAACGTATTGGATTAGCCCTATCAACACGGCAGTAGACATGGATTGCATGA

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|22009263|gb|BQ794297.1|BQ794297
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|46919589|gb|CN548918.1|CN548918
EST:     TCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: TCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|161713392|gb|FC062791.1|FC062791
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|110707546|gb|EE084067.1|EE084067
EST:     GTTATCGGATGGCCCANGATTTCTTCAATGCACATATTANTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|161706380|gb|FC056758.1|FC056758
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|33408862|gb|CF214489.1|CF214489
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|33408377|gb|CF214004.1|CF214004
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
EST: gi|33408634|gb|CF214261.1|CF214261
EST:     GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAG                         TCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG
genomic: GTTATCGGATGGCCCAGGATTTCTTCAATGCACATATTAGTCCCATACAGgtaaacaaac ... ttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC
             tctttatcttttattt  CT-rich tract
            atctttatcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagcgtaaagattcctcaaccatgtgttaatcttctttctttccaagtatggttcatctttatcttttatttcttttgcttttcttttttctttacagTCGGGATGCTGTAAGCCACCAACTGAATGCGGGTACACCTTTGTGAATCCGAGCTATTGGATTAGCCCCATATACACAGCAGCGGACATGGATTGCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - gtaaaga
- - - - - - - - -tcaacca
- - - - - - - - - - - - - - - - - - - - - - ccaagta