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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggttatacttgaaatttgtgctctctctttgcagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt...

Basic information

species Vitis vinifera
transcript Vv07s0031g01620.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 5'ss of exon 6
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagtt--ggttatacttgaaatttgtgctctctctttgcagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt---
| || || ||||||||| |||| |||||||||||||||| || |||||||| || |||||||| || || ||||| ||||| |||||||||||||| ||||| ||| | | | || | | | | || || || | | ||| | | | | || || | ||| | | | ||
CAGCAAGGACATGCAATGTCATTCTGATTGTTCTTGATGCCATTAAGCCAATAACCCACAAGCGGCTTATTGAGAAGGAGCTTGAGGGATTTGGCATTAGgtatgttttgactttcttttgggtagaagatgtttca--gcggtgtttgc-catactatacaaaacttgctaagggtgcg--ttcggcggtgagagttcccaact

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 6
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggttatacttgaaatttgtgctctctctttgcagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt---------
| ||||| ||||||||| |||||||||||||||||||| ||||| ||||| |||||||||||||| || ||||| ||||| || ||||||||||| |||||||| | ||| | ||| | || || | || || | | | | | | || ||| | ||| || ||
CAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGATTTGGCATTAGgtaagtc-----ttctttacattcatacttctgct----ggcgctagtgtacgaaacttgtacacagcttggccatcagtccttttgtgatctttcctttgctcccaat

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 6
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggt-tatacttgaaatttgtgctctctct---ttgcagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt
|||| || ||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||| |||||||||| | | || | | | | |||| | | | || | | | | ||| | | | | ||| ||| || || | | |
CTGCAAGGACATGCAATTGCATTTTGATTGTCCTTGATGCAATAAAGCCAATAACTCACAAGCGTCTTATAGAAAAAGAGCTAGAGGGATTTGGTATAAGgtaaggtaacatgtaaattgattatttgctatttttatgttacgtcaccaatattctgatttctaaacaaggcaggggtct--cttataattgtttaccact--

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 6
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggttatacttgaaatttg-tgctctctctttgcagttctggt-tcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt-
|||| |||||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| || || |||||||| ||||||||||| ||||||||| || | ||| | ||||| | | | || | | | | | ||| | |||| | | | ||| || | ||| ||
CTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGATTTGGTATAAGgtaacatg-taatattgattatttgctatttttatgttatgttaccaatattctgatttctgaacaaggcaagggtctcctcttataatttttt--cccattg

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 6
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgt--aagttggttatacttgaaatt---tgtgctctctctttg--cagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt
| ||||| |||||||| ||||| || || ||||||||||| ||||| |||||||||||||||||||| || || ||||||||||| ||||| || ||||||| | ||| ||||| || | | || | | |||| | ||||||| || | | | || | | | | ||| |
CGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGATTCGGAATAAGgtatagattgtttatataacaacctttatacactgtatatttgatcgtttctggtagatagtct-----gactcgatcatggactgttgctatgtag----------

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|28970187|gb|CB349220.1|CB349220
EST:     ATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAG                         GTTAAACAAGGAACCACCAAATCTGACCTTCAGGAAGAAAGATAAGGGTGG
genomic: ATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggt ... ctggaaacagGTTAAACAAGGAACCACCAAATCTGACCTTCAGGAAGAAAGATAAGGGTGG
EST: gi|71857454|gb|DT006509.1|DT006509
EST:     ATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAG                         GTTAAACAAGGAACCACCAAATCTGACCTTCAGGAAGAAAG
genomic: ATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggt ... ctggaaacagGTTAAACAAGGAACCACCAAATCTGACCTTCAGGAAGAAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGATTTGGCATAAGgtaagttggttatacttgaaatttgtgctctctctttgcagttctggttcatttttttggggaaaggtatagcgtccagcttctacctgaaaaacccctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaac