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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag

Basic information

species Vitis vinifera
transcript Vv05s0077g00140.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 5'ss of exon 14
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 || ||||| || || ||||||||||||||||| || ||||| || || || || ||||||||||||||   ||||||||| ||||| ||||| || ||||| || |   |    ||| |      |    | |      | |     || ||  || |  | ||   | ||||    |   || |||
GGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTGTTTATGGGACCAAGgtaaatagcaaa---ttagatcaatcaacagtacacaacatatat--ttgctttgctaat-tcatg-cactcacacatttgcat-cag

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G007229_T01 (Zea mays), 5'ss of exon 13
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaaca-aataggattta--aaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 |||||||| ||||||||||| |||||||| || || ||||| |||||||| || ||||||||||||||    |||||||||||||| ||||| || |||||    | || |  ||| |  |||   | |    |    | || ||   ||| |    |||    |  | |||  |               
AGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTGTTTATGGCACTAAGgtcggtagaaaactattcaataaacaaagaggtatggcggattgctaaggctttcattctgg---tgaactatatag--------------

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G353548_T01 (Zea mays), 5'ss of exon 13
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggttt-ctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 |||||||| ||||||||||| ||||||||||| || ||||| || ||||| || |||||||||||||     |||||||||||||| ||||| || ||||||   |   |   | |  |||  | |        ||||    |||   || |||  |     |  | |||  |               
AGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTGTTTATGGGACTAAGgtgggtag-caaattattcaataaacaaaaaggtatggtggattgctaatgcttaaattgtggtgaattatatag--------------

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G353548_T04 (Zea mays), 5'ss of exon 13
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggttt-ctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 |||||||| ||||||||||| ||||||||||| || ||||| || ||||| || |||||||||||||     |||||||||||||| ||||| || ||||||   |   |   | |  |||  | |        ||||    |||   || |||  |     |  | |||  |               
AGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTGTTTATGGGACTAAGgtgggtag-caaattattcaataaacaaaaaggtatggtggattgctaatgcttaaattgtggtgaattatataggaag----------

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 5'ss of exon 13
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatgga-tattgcttcttggtttctg-----cagctgt--ttacctgaccttataatattcacttgctcaaatacag----
 |||||||| ||||||||||| ||||| ||||| |||||||| || ||||| || || ||||||||    ||||| || || ||||| |||||||| |||||||     |    | |    |||| || |  ||     | | ||     ||| |||  ||   |    ||  || ||||  |  || | ||| ||    
AGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTGTATATGGAACAAAGgtgagttgttcttctgtgttctggactagtatttagatatatgtgtgaatcagttgtagttctatactgtttgaagattcgttatctgagataaagtgtt

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 5'ss of exon 12
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaata-------ggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag-------
 |||||||| |||||||| ||  | |||||||| || |||||||| ||||| || |||||||||||    ||||| ||||| ||||  |||||||| |||||||      |       |  ||| ||     || |   |  |    | || ||  || | |||    |||  | ||| | |   | |  |  |        
AGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTGCATATGGAACAAAGgtgagttgtgattcctctgtttttcaagccagtaataagttatcacat-tgtaggagtct-ccttttgttagtagatttattgtttaagctggaatattttg

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: EFJ26270 (Selaginella moellendorffii), 5'ss of exon 13
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 ||| || |||| ||| ||||||| || ||||| || ||||| ||||||||||| ||||||||||||   ||||| || || ||||| || || || |||||     ||      || | ||||||    |  | |  |     ||  |                                       
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgttcggcaactttccttgagatggatgactcggcctaatgc--acaaataacag----------------------------------

upper sequence: Vv05s0077g00140.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: EFJ14567 (Selaginella moellendorffii), 5'ss of exon 12
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag
 ||| || |||| ||| ||||||| || ||||| || ||||| ||||||||||| ||||||||||||   ||||| || || ||||| || || || |||||     ||      || | ||||||    |  | |  |     ||  |                                       
AGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTGTTTACGGCACAAAGgtttgacaactttcctttagatggatgactcggcctaatgc--acaaataacag----------------------------------

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|18459486|gb|BM437764.1|BM437764
EST:     TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACAAAG                         GAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
genomic: TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaat ... tcaaatacagGAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
EST: gi|30129161|gb|CB914500.1|CB914500
EST:     TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACAAAG                         GAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
genomic: TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaat ... tcaaatacagGAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
EST: gi|30321258|gb|CD004520.1|CD004520
EST:     TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTTTATGGAACAAAG                         GAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
genomic: TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaat ... tcaaatacagGAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
EST: gi|30125879|gb|CB911218.1|CB911218
EST:     TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACAAAG                         GAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
genomic: TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaat ... tcaaatacagGAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
EST: gi|32457197|gb|CD798371.1|CD798371
EST:     TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACAAAG                         GAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT
genomic: TAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaat ... tcaaatacagGAAGGGAAACTCAGAATCCTCCAATATGATAGTTCTCATGGCATGAATTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTGTCTATGGAACGAAGgtgaacaaataggatttaaaatggatattgcttcttggtttctgcagctgtttacctgaccttataatattcacttgctcaaatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG