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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag

Basic information

species Vitis vinifera
transcript Vv09s0002g03680.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcatt--gactccag-----------------
|||||||||||||| |||||||||| |||||||||||||| | || ||||||| || |  ||||| || || || || || ||||| |  |||   ||    ||   ||        | |   |     |   ||   |      | |  |  ||| | |||||     ||| |                 
GAATGGATAATGGATCAGTGGGAGAGAAACTTCTATATCACTTCATTAGCAGGTGCAAACAATGGCAGTTCTCTGGTGGTCATGTCAAGAGgtatatcattgattcctgctctcaataataagacatgcactcttgcatgccaagtaccaggattcctatcattttatgtcctggctttgtggttctgtgg

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G158177_T01 (Zea mays), 5'ss of exon 6
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGg---ttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag-------------------
||||||||||||||||||||||||| ||| |||||||||| |||| | || || || | |||||| |||||  | ||  | ||||| |  ||   ||||| ||| || ||||          ||  |   || ||  ||  |       |  | |  ||||| |||    || ||                   
GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGGGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattagtgtaa-atgtttgagcttgatgcttagactgcagaacatacttggtgacag--taaaatcattgcatattatctagtgtcaagatgcatctcaca

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag----------------------
||||||||||||||||||||||||| ||| |||||||||| |||| | || || || | |||||| |||||  | ||  | ||||| |  ||| | |  |   |||    | | | |  |||  |       || ||||    |   ||      | |      || ||||                       
GAATGGATAATGGAACAGTGGGAGAGAAATTTCTATATCACTGCACTGGCTGGTGCGAATAATGGAAGCTCTTTGGTGATTATGTCAAGAGgtaattacatggtatcatccaggttgccttccgttt---gtttcatctgccctagcctctttcccgtgctgcggattccacggctgtgcgttcacaacacccg

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttgg---ctgatggatt--tctatgacaaaatttatctata--ttttgcttgacttcatttcattgactccag------------
||||||||||||||||| |||||||| ||||||||||||| |||  ||||||| || |  ||||| || ||||| || || ||||| |  ||| |  | |   |   | |    ||    | |  |   ||  ||||||     |||  |||| | || || | | |  |  | |   |            
GAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaatggtgcctaggatttgtaaaactacttcctgttaaaattgtgtaataattttttcgtgtctacctattgtaaaattgtgtgtacaaagttc

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagt----ctaacatatttggc--tgatggatt-----tctatgacaaaatt--tatctatattttgcttgacttcatttca-ttgactccag--------------------------
|||||||| ||||||||||||||||| || |  || || ||||| ||||| || |||| ||||||   |||| | |||||||||||||| ||||| |    || |  | |||     | ||| |||     | |  |     | |  |||  ||||||||  ||  |   ||| | ||| || |                            
GAATGGATTATGGAACAGTGGGAGAAGAATTATTACATTAGTGCCATAGCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttag

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtc---taacatatttggc--tgatggatt---tct-----atgacaaaatttatctatattttgcttgacttcatttcattgactccag------------------------------------------------------------
|||||||| ||||||||||||||||| || |  || || ||||| ||||| || |||| ||||||   |||| | |||||||||||||| ||||| ||   | |  |||||     | ||| |||   |||     ||| | | | ||  ||  | |||   |||   ||| |  |||  |                                                                
GAATGGATTATGGAACAGTGGGAGAAGAATTATTACATAAGTGCCATAGCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatgatcacatgtt-ttgcttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattgatccttttag

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgt------tagtctaacatatttggctg---atggatttctatgacaaaatttatctatattttgcttgac--ttcatttcattgactccag----------------------------------------------------------------------------
|| ||||| |||||||||||||| || || ||||||||||||||||| || ||||||| ||||||||||||  | || || ||||| || |||      | |  ||  ||  || | ||   || || |    |  || | || ||||  |   || ||||   || |||    | | |                                                                                
GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAGgtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtag

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 13
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgac-tccag--------------------
|| ||||| |||||||||||||| || || |||||||||||||| || || || || | ||| || |||||  | || || |||||||| ||| | |  | |  || |  |   | ||||   |  |  |  || ||  |||| |   |  | ||  | |  ||  | | | |                    
GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgt-atttcacccgatgttacatttagattaacactatcat-ttcatgcatatgtacttcaattttttatttttatcatgctgcttaatttttgtagatttat

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 5'ss of exon 11
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag
|| ||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |  || || ||||| || ||||| ||||| || ||| | | |  |   | |   ||||||                | |    |  ||  |  |                     
GAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAGgt-attgtcgc---tgttattgatggccactggcattgttgctgacgcgtgattcccccgcag------------------

upper sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 5'ss of exon 11
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag
|| ||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |  || || ||||| || ||||| ||||| || ||| | | |  |   | |   ||||||                | |    | |||  |  |                     
GAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAGgt-attgtcgc---tgttattgatggccactggcattgtcgctgacgcgtgtttcccccgcag------------------

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|71885940|gb|DT034995.1|DT034995
EST:     TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG                         GTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
genomic: TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaa ... ttgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
EST: gi|156737302|gb|EV241423.1|EV241423
EST:     TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG                         GTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
genomic: TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaa ... ttgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
EST: gi|161714228|gb|FC064143.1|FC064143
EST:     TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG                         GTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
genomic: TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaa ... ttgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
EST: gi|71881724|gb|DT030779.1|DT030779
EST:     TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGG                         GTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA
genomic: TGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaa ... ttgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGGATAATGGAACAGTGGGAGAAAAACTTCTATATCAGTGCAATAGCAGGAGCTACTAATGGGAGCTCACTAGTTGTAATGTCTAAGGgttagtctaacatatttggctgatggatttctatgacaaaatttatctatattttgcttgacttcatttcattgactccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA