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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg...

Basic information

species Vitis vinifera
transcript Vv04s0210g00180.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttagga-cataaagtcaatgaacccg-----------
|| || || ||||||||||||||| | ||||| || || || || ||||||||||| ||||| || |||||||| |||||||       |||||  |  |     || |   ||  |  ||||  ||   |      ||||      |||  | | |||| |   ||  | |    |  |           
GTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAGgta-------aattttgaactatcgcttgtaattctgtacttttacctgcac-----aaatagtcaatacggctatcaggagctggaaaccgacaggcttgcttttgcagtt

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G006672_T01 (Zea mays), 5'ss of exon 2
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcct---ccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg
|| || || ||||||||||||||| | ||||| |||  ||| || ||||||||||| ||||| || |||||||| |||||||   |  ||| |   | ||   | | || | |   | | ||   |   |  | || |  ||  |  |  |    |    |  ||||| | | ||    || 
GTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAGgtagggtttcaactatgatttatgaatcctacatatgcaaataacatacttggttttatgtaaagttgt--atttgttaaggcccataaggcccatattgcc-

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcac-aatttcaagtttatatttcttcctccattatttttt-----cttttcttctagaatatcatccacgcat-cttaggacataaagtcaatgaacccg
|| || || ||||||||||| ||| |||| |||||||| ||||| || |||||||| ||||| |||||||||||||||||||   |    | || | | | |||  |   | |    || |  | |      ||  | | |  |||| | |||  || |  ||    |||    |||||       
GTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgttagttactactgtattgtaacttcagtgttctcatctgattatttgcccttttaaatacc-tccttgcttgtttctaccatgttatcaatt------

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatct-taggacataaagtcaatgaacccg--
|| || || ||||||||||| ||| | || ||||||||||| || ||||||||||| ||||| ||||||||||| ||||||||| |    ||||| | | |||   |    ||| |  |||||   ||   | |     |||  | |   || ||   |   |   | || |||    |   
GTAACCCCCAATCTTTATGGAAATCTTGTTGCAAATACAGCGGCAGGTATTGCTGGAGGCACTGGAGTCATGCCGGGAGgtatagttcttatttctaatatat---tgaagctctagaattttaatttgattacattgctatttttcttacaactactgtctaattactccatgtcgtcatt

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcac-aatttcaagtttat----atttc--ttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg
||||| || ||||||||||| ||| |||| ||||| || ||||| || |||||||| ||||| ||||||||||||||||||| | |    | || | | | |||    | |||  | |   |||    || | ||   || |  |||| |  |        ||    |||    |||||       
GTGACCCCAAATCTTTATGGAAATCTAGTTGCAAACACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacagttgttagttgctactgtattgtaacttcagtgctatcatctgattatgttgctttttcaaataccgccttgctcatttctaccatgttatcaat-------

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatact-cacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg-------
|| ||||| ||| | ||||| |   | ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||  || | | ||||||   | |||| ||       || | |||| |||       |  | |   |  | |   ||||| |||||       |  ||  |       
GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATTGCAGGCGGAACTGGAGTCATGCCTGGAGgtaccctactccatttcattataatatctc-------ataacttttgcttcaaaataatcaaagactgta-gtgacttagtacatatttctttttcacttggagcacc

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 3
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatc----ttaggacataaagtcaatgaacccg
|| ||||| ||| | || || | ||| || || ||||| |||||||||||||| || || || || |||||||||||||||||   |     ||  | |||  |  |  |  |  || | | |       |    |  |  |  | |  |  |     || |     ||| |||    ||   
GTAACACCAAATTTGTACGGAACTTTGGTAGCCAATACCGCAGCTGGTATTGCAGGCGGAACTGGTGTCATGCCAGGAGgtatgtccgtttgttttatttttcagcttcttgtt-atcactgtaatagaccgatgaagaccttgttctagtcttgtttttggagttcaaactcagatgac---

upper sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 4
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg-
|| ||||| ||| | || || |  || || || ||||| ||||| |||||||| || ||||| || ||||||||||||||||   ||     ||  | ||| || |  |||  | ||   |  | |  |  |    ||| ||| | ||  | |  | |     | | | | |  ||    
GTAACACCAAATTTGTACGGAACCTTGGTAGCTAATACCGCAGCCGGTATTGCAGGCGGCACTGGTGTCATGCCAGGAGgtactttcgttcgtttta-tttttagtctttctacaatctatgctacactgatgaaggaagatcgtacaaccttactggacttcagatttatttgacaatt

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|110702504|gb|EE081292.1|EE081292
EST:     GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAG                         GCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGA
genomic: GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcac ... gtgtttgcagGCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGA
EST: gi|110415520|gb|EC981433.1|EC981433
EST:     GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAG                         GCAATGTTGGGGCTGATCATGCTGTTTTTGAGCAAGGTGCTTCAGCAGGGA
genomic: GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcac ... gtgtttgcagGCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGA
EST: gi|71888801|gb|DT037856.1|DT037856
EST:     GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAG                         GCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGA
genomic: GGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcac ... gtgtttgcagGCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAGgtatactcacaatttcaagtttatatttcttcctccattattttttcttttcttctagaatatcatccacgcatcttaggacataaagtcaatgaacccg

- - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagtcaa