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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG

Basic information

species Vitis vinifera
transcript Vv02s0087g00170.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G35390.1 (Glycine max), 3'ss of exon 9
gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG
| ||||| | | ||| | | | | | | |||| | |||| ||| || || ||| | || ||||| || || | | | | || | || |||||||||||||| ||||||||||||||| | ||||| ||||||||||| |||||||| || || ||||| |||||||||||||||||||| || |||
---gttttctccttatctctctgcagctttca---tatagacctatttgagtaatcttttttcta--ctttacattgaaaaatccttaaaacttggaatgccca---aaatgtcttgta------gGTGCATCAATTGTGATGTTTCATGGAGACTTACCATATTCTTCAAAAGACATCATCAAGAAACTAGAGACTTTGAATGAGGAACACATAATAGGGATAGG

upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G34940.1 (Glycine max), 3'ss of exon 10
gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG
||| | | ||| || | | | | || |||| | | || ||| || || ||| | || ||||| || ||| | | | | || | || |||||||||||||| |||||||| |||||||| ||||| ||||||||||| ||||| || || || ||||| |||||||||||||||||||| || |||
-----gtttactctatctctctgtagcttgcatacaga---cctatttgagttatcttttttcta--ctttacattgaaaaatccttaaa---aattagaatgcccaaaatgtcttgta------gGTGCATCAATTGTGATGTTTCACGGAGACCTACCATATTCTTCAAAAGACATCATTAAGAAACTAGAGACTTTGAATGAGGAACACATAATAGGGATAGG

upper sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G31420.2 (Arabidopsis thaliana), 3'ss of exon 10
--gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG
| || || | || | || || | || | ||| | ||||||| | |||| |||| || || | | |||| | | || | || || | | ||||||||| || ||||| ||||| || ||||| | || |||||||| ||||||||||| || |||||||| | |||||||| || ||||||||||| | ||
gtgagccgtattgattttttttgtacaga-tattatctcgttaaatattggg---aaattt--catatttttctctatct-----cctaaatcttcattgtgactttt-----------tcaattcagGTGCGTCTATTGTGATGTTCCACGGAGATTTACCTTACTCTTCCAAAGATATCATTAAGAAGCTGGAAATGTTGAATGAAGAGCACATAATTGGATGTGG

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|161707249|gb|FC055597.1|FC055597
EST:     AAAATTTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAG                         GTGCATTCAATTGT-ATGTTTCATGGAGACCTGCCATACTCTTCAAAAGAT
genomic: AAAATGTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAGgtgctgttct ... ataacttcagGTGCAT-CAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGAT
EST: gi|110696915|gb|EE073446.1|EE073446
EST:     AAAATTTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAG                         GTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATA
genomic: AAAATGTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAGgtgctgttct ... ataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATA
EST: gi|122689621|gb|EC941876.1|EC941876
EST:     AAAATTTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAG                         GTGCATCAATTGTTATGTTTCATGGAGACCTGCCATAATCTTCAAAAGATA
genomic: AAAATGTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAGgtgctgttct ... ataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATA
EST: gi|110687636|gb|EE065268.1|EE065268
EST:     AAAATTTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAG                         GTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATA
genomic: AAAATGTGGTAAAAATGATGGCAGGAGTCTTGCAATGGATGTTAGTGGAGgtgctgttct ... ataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG
                                      aagttatataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgttctcataactattctataacctactgtctgaatgtttattgggctaatatttattatatccttgtccttttgggatcctagaattcaatcatatctattgacaagttatataacttcagGTGCATCAATTGTTATGTTTCATGGAGACCTGCCATACTCTTCAAAAGATATCATCAAAAAGCTGGAGACATTGAATGAGGAACACATAATTGGTTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA