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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttccttcattcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga...

Basic information

species Vitis vinifera
transcript Vv17s0000g09910.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G094978_T02 (Zea mays), 5'ss of exon 1
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttccttc-attcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga
    ||  ||||  |||| ||  | || || || ||||| ||||| || || |||||||| ||||| || ||||||||||||||||| || ||||||||||| |  ||||||| || | | | |   ||  | |   |||| || |   |   |  ||  | |   ||  | |||| ||   |   | || |   ||||  
CGGTGCCTTTCCGGCGGCGCTGTTGTTCGATTGCGATGGTGTGCTGGTGGACACTGAGAAGGATGGCCACCGCATCTCCTTCAACGAAACCTTCGCCGAGgtccaattccttccatccgtactcccgttcatctccattttcttgatg-cagctgcttccactatgttaatcttttctgcggtacctatgctcctagttat

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 1
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcctt-cattcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga
|||  ||||||| |||||||| || |||||||||||||| || || || ||||||||||||||||| |||||||| || |||||| | || |||   ||||| | |||   |  ||  |      |||      ||||   ||   | |||  | |    |  |    | |  || |     |    |||   ||      
TTCCACTCTTCCCTCGGCTCTTCTATTTGACTGTGATGGAGTCCTTGTGGATACTGAGAAAGATGGCCATCGCATATCTTTCAACCAAACCTTCCAAGAGgtacacttatatatatatagtatagtatacactcttttccattgagcatctcgtataaccatgttggagttgcttaactctcttttcgtggactctacaa-

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA06G18320.1 (Glycine max), 5'ss of exon 2
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgccc-ttccttcattcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga-
|||  ||||||| || ||||| || |||||||||||||| || || || |||||||||||||||||||| ||||| || |||||| | || |||   |||||     |      |   |  | | ||    ||||    ||| ||| ||| |||| |     |||      ||   |||  ||  |    |||  |  | | 
TTCCACTCTTCCCTCAGCTCTTCTATTTGACTGTGATGGAGTCCTTGTGGATACTGAGAAAGATGGTCACCGCATATCTTTCAACCAAACCTTCCAAGAGgtaaatatgtacctacctacactcataaccttgttgaagtttcttaactcattttgtagacttta--caaattacaatgctatatggaacttaagaacttaa

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 1
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttccttcattcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga
  |  ||||||| || ||||| ||||| || || ||||| || || || ||||| ||||| || |||||  | |||||||||||||||||||||   |||||  |     || | |          |||  ||  ||   | ||| ||    |  |  || ||      | ||||   |                     
GACGACTCTTCCCTCTGCTCTTCTCTTCGATTGCGATGGCGTTCTTGTTGATACCGAGAAGGACGGTCACAGGATCTCCTTCAACGACACTTTCAAAGAGgtttctcagttttagtt---------ttttggtcattagctcttagcttcggtgatgataattgg--aatcttttgcag---------------------

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|351049437|gb|FQ450038.1|FQ450038
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351046213|gb|FQ442591.1|FQ442591
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351046860|gb|FQ454470.1|FQ454470
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351048691|gb|FQ448965.1|FQ448965
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351053962|gb|FQ441728.1|FQ441728
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|110361698|gb|EC925191.1|EC925191
EST:     ACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351031800|gb|FQ460057.1|FQ460057
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351039737|gb|FQ464775.1|FQ464775
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351054042|gb|FQ441808.1|FQ441808
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
EST: gi|351031985|gb|FQ460242.1|FQ460242
EST:     ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAG                         AGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA
genomic: ATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttcc ... gaatgaacagAGAGAATTGGGTGTTACCTGGGATGTGGACTTGTATGGCGAGTTGCTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCTCTTCCATCGGCTCTCCTCTTTGACTGTGATGGGGTGCTCGTCGATACTGAGAAAGATGGTCATCGCATCTCCTTCAACGACACTTTCGCCGAGgtgcccttccttcattcatccgcttatttctgttttttttttttacctcttttttttttagttaattggttttttatggaatgggtgtgttatcagttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG