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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccttatagtgatttacgttttcataagttgttggattcatttcccctctctgctcttcaagtaatgcaattcatctcagattagtaacttttttagaggcaaatccagtctaccatcttccccatcagtctgtctggatgtacagatgttgtgctgtgctgatggtttttgctttctgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGAAATCTAGAGATCCGGCATCGCAAGTGCCCAGCTTGTGGAACTGCATTTG

Basic information

species Vitis vinifera
transcript Vv06s0004g00950.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00950.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA14G05490.1 (Glycine max), 3'ss of exon 8
gtaaaccttatagtgatttacgttttcataagttgttggattcatttcccctctctgctcttcaagtaatgcaattcatctcagattagtaacttttttagaggcaaatccagtctaccatcttccccatcagtctgtctggatgtacagatgttgtgctgtg-----ctgatggtttttgctttctgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGAAATCTAGAGATCCGGCATCGCAAGTGCCCAGCTTGTGGAACTGCATTTG
| ||| || | | || | | | | | | ||| ||| || | || ||| || | |||| | | | || ||||||| || || || |||||||||||||||||||||||||||||||| || |||||||||||| | ||||| ||||| || || || |||||||| |||||||
---------------------------------------------------------------------------------------------tcctttcttgg-acttgcactgcatggttatacgtagtagt--atctagaatagaatatattgcaacagaaacacctaaaagtttgatgtgtgtatttggcagGTTGTGATTGTCAAGTGCTATCATCTGTTCTGCAATCCATGCATTCAGAGAAATCTAGAGCTTCGGCACCGCAAATGTCCTGCATGTGGAACAGCATTTG

upper sequence: Vv06s0004g00950.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA02G43490.1 (Glycine max), 3'ss of exon 19
gtaaaccttatagtgatttacgttttcataagttgttggattcatttcccctctctgctcttcaagtaatgcaattcatctcagattagtaacttttttagaggcaaatccagtctaccatcttccccatcagtctgtctggatgtacagatgttgtgctgtgctgatggtttttgctttctgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGAAATCTAGAGATCCGGCATCGCAAGTGCCCAGCTTGTGGAACTGCATTTG
|| ||| || | | | | | | || | || |||| | ||| | ||| | | | || | |||| | | || ||||||| || || || |||||||||||||||||||||||||||||||| || |||||||||||| | ||||| ||||| || || || |||||||| |||||||
----------------------------------------------------------------------acatcctttcttggacttgca------ctgcatgtttatacgtagtagtatctag------attctatatggcaacaaaaacac---------ctaaaagtttgatgcgtgtatttggcagGTTGTGATTGTCAAGTGCTATCATCTGTTCTGCAATCCATGCATTCAGAGAAATCTAGAGCTTCGGCACCGCAAATGTCCTGCATGTGGAACAGCATTTG
















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|110362164|gb|EC925680.1|EC925680
EST:     ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAG                         GTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
genomic: ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAGgtaaacctta ... tgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
EST: gi|32249956|gb|CD715775.1|CD715775
EST:     ATGGCAAGGCAATTCTGANATGCGGTGTGTGTTTTGACCGGCCAAAGGAG                         GTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
genomic: ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAGgtaaacctta ... tgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
EST: gi|110370378|gb|EC929549.1|EC929549
EST:     ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAG                         GTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
genomic: ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAGgtaaacctta ... tgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGA
EST: gi|27579894|gb|CB002589.1|CB002589
EST:     ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAG                         GTCGTAATCGTGAAGTGCTATCATCTGTTCTGNCA-TCCATGCATCCAAAG
genomic: ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAGgtaaacctta ... tgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTG-CAATCCATGCATCCAAAG
EST: gi|27581325|gb|CB004020.1|CB004020
EST:     ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAG                         GTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAA
genomic: ATGGCAAGGCAATTCTGAAATGCGGTGTGTGTTTTGACCGGCCAAAGGAGgtaaacctta ... tgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctggatgtacagatgttgtgctgtgctgatggtttttgctttctgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGAAATCTAGAGATCCGGCATCGCAAGTGCCCAGCTTGTGGAACTGCATTTG
                         tgctgat  putative branch site (score: 3)
 tttttgctttctgtt  putative PPT
 ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccttatagtgatttacgttttcataagttgttggattcatttcccctctctgctcttcaagtaatgcaattcatctcagattagtaacttttttagaggcaaatccagtctaccatcttccccatcagtctgtctggatgtacagatgttgtgctgtgctgatggtttttgctttctgttgggcagGTCGTAATCGTGAAGTGCTATCATCTGTTCTGCAATCCATGCATCCAAAGAAATCTAGAGATCCGGCATCGCAAGTGCCCAGCTTGTGGAACTGCATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC