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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctatcacgcacatgcacatacacacacacacactcactttatctagggtatgtattgataaattagaatgattct...

Basic information

species Vitis vinifera
transcript Vv14s0068g00420.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00420.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G26860.1 (Glycine max), 5'ss of exon 10
GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctat-cacgcacatgcacatacacacacacacactcactttatctagggtatgtattgataaattagaatgattct
|||  |||||||||||||||| ||||||||||||||  ||||||||||| |||| || ||||| |||||  | || ||||||||||| ||||| ||||| ||     |||||||||| |||||||| |  ||||||||  || ||    |       | ||| || | ||     |   |   |   ||  |||   | | 
GAGACTGATAGATCCTCAAGGGAAACCAACAGGAGTGATGGGATGGTGGGCTTCTCGTGCTGTTACATTCCTAGAGAACCATGATACCGGGTCCACACAAgtatgaactctctctctttctctctccacacacgcacactcatatgtttatcttttgattcatttga-ctctcacactcaagtacttatgggaaatttccc

upper sequence: Vv14s0068g00420.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S342_20V6.1 (Physcomitrella patens), 5'ss of exon 15
GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctatcacgcacatgcacatacacacacacacactcactttatctagggtatgtat-tgataaattagaatgattct-----------------------------------------------------
||| ||||||||||||||||| |||||| | |||||  |||| ||||||||||| || || ||||| ||  | || |||||||| || || ||||| ||||||  | |||| |||  |  |||     | |   |  ||   |  |  |   |   | | |  | || |  |   |||||   | |||  |  |  ||  |                                                     
GAGATTGATAGATCCTCAAGGGAAACCACCCGGAGTGATGGGCTGGTGGCCTTCTCGTGCAGTCACGTTCCTTGAGAACCATGACACCGGATCAACGCAGgtttgcactctatctaccattctagacttgatctatttg-gtaaccgtaagtatctagttagataattttagtcctgtatgctacaaaccactacaatcgtcgtccttgagtacttgacatgaccctgatagtgccatacgttactgttttcag

upper sequence: Vv14s0068g00420.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S100_191V6.1 (Physcomitrella patens), 5'ss of exon 12
GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctatcacgcacatgcacatacacacacacac----actcactttatctagggtatgtattgat-----aaattagaatgattct-----------------------------------------------------
||| || ||||||||||||||||||||| | |||||  |||| ||||||||||| || || || || ||  | || || || ||||| || ||||| ||||| ||||  || |  |  ||| ||  |   | ||   || ||  ||   |  | |     |  || | ||  |   |||  || | ||     ||  |  | ||||  |                                                     
GAGATTAATAGATCCTCAAGGAAAACCACCTGGAGTGATGGGTTGGTGGCCTTCTCGTGCAGTTACTTTCCTTGAGAATCACGATACCGGATCAACTCAGgt-ctctacct-taacattctgtcagtgatatgcctctggacgaactgtctgaaattgaaatacaatatacatgatgtagatacttatgttgtaagcttcagtgatcttcataattgagcacttgccatgccgctaacattggcacatggtgccgtctccag

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|110428475|gb|EC994949.1|EC994949
EST:     CTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAG                         GGTCATTGGCCATTTCCACGAGATAAGCTTACACAGGGATATGCATACATT
genomic: CTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctc ... tttatttcagGGTCATTGGCCATTTCCACGAGATAAGCTTACACAGGGATATGCATACATT
EST: gi|110413904|gb|EC979720.1|EC979720
EST:     CTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAG                         GGTCATTGGCCATTTCCACGAGATAAGCTTACACAGGGATATGCATACATT
genomic: CTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctc ... tttatttcagGGTCATTGGCCATTTCCACGAGATAAGCTTACACAGGGATATGCATACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTTGATAGATCCTCAAGGAAAACCAACAGGAGTAGTGGGATGGTGGCCTTCACGCGCTGTCACATTTTTGGAAAACCATGATACTGGGTCAACACAGgttctctctctctctctctctctctctatcacgcacatgcacatacacacacacacactcactttatctagggtatgtattgataaattagaatgattct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgataaa