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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatgattttgtttctccaggatttgcatatttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG

Basic information

species Vitis vinifera
transcript Vv12s0028g01810.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 4
gtatgtaatgattttgtttctccaggatttgcatatttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
|| |||       |  |   ||    ||||  | ||   | | ||  || |    ||   |    |    | |  | | ||  |   ||| | ||||||||||| || || |||||||| || || ||||| || ||||||||||||||||| ||||||||| ||
gtgtgtggattgctaatcaatcataaattttgaaatgcctgccttcctg-tgtgtctcttctaagt--ctattctacattggctg--cagTTATTTAGGGGGCTTGCGTACATTCATACTGTTCCAGGGGTCTGTCATAGGGATGTGAAGCCACAAAATGTTTTG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 3
gtatgtaatgattttgtttctcca---ggatttgcatatttttcct--tttttggtactcctgac-cctgatagtaagtga---aaaatgct-taatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
|||||   |  | |   ||  | |    | ||   || || ||| |  |  |   | ||  |||    |  || | | |||      |||   |    |||| |||||||| ||||| ||||| || || || || ||  ||||||||||||||||||||||||||||| || | 
gtatgaggttttctctgtttgcaatttagtttgatatgttgttcttgctcctcaattcttttgaaattttgtaatgattgagttgggatgtgatgtctagATCTTTAGGGGACTGGCGTATATCCACACTGTACCAGGAATTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTA

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 4
gtatgtaatgattttgtttctccaggattt-gcatatttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
||||| | |  | |  | | |   | |||| ||  || | |  |||| |   | |  | ||  |   |||  |   |  ||| |||    ||| ||||||||  | || ||||| ||||| |  |  || |||||||||||||||||||||||||||||| || ||
gtatgaacttttctattctgtttggaatttagctcatgtgttgttttataacattg-taacaatcg-agtttggatatgatgttta----gATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 4
------------gtatgtaatgattttgtttctccaggatttgcatatttttccttttttggtactcctgaccctgatagtaagtgaa---aaatgcttaatc-agATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
             | |||    | |||| ||    | | | | | | ||  ||  |||||     |    |   | ||| | | |||      |||     || |||| |||||||| ||||| ||||| ||||| || || ||  | |||||||||||| |||||||||||||| || ||
gtatgaggttttctctgttggcaatttggtttgatatgttgttcttgttcctcactttttc---ttttgaaattttataatgattgagttgggatgtgatgtctagATCTTTAGGGGACTGGCGTATATCCATACTGTACCAGGAATCTGCCATAGGGATTTGAAGCCTCAAAATCTTTTG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 4
gtatgtaatgattttgtttctccaggatttgcatatttttccttttttggtactcctgaccctga---tagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
    |||   | | |  |  || | | || | || |  ||| | | ||| |  |  | ||  ||    || | |||    |     |  | |||| || |||||  | || ||||| ||||| |  |   | ||||||||||||||||| |||||||||||| || ||
----gtatgaactcttctattctatgtttggaatttagttcatgtcttgtt--ttataactttgtaactattgagtttggatatgatgtttagATCTTCAGGGGATTAGCATATATCCATACCGCCCTGCGAGTTTGCCATAGGGATGTAAAGCCTCAAAATCTTTTG

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|37185091|gb|CF604444.1|CF604444
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|110711443|gb|EE087924.1|EE087924
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71860504|gb|DT009559.1|DT009559
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71857679|gb|DT006734.1|DT006734
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATACCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|110725002|gb|EE101323.1|EE101323
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|349830587|gb|FQ416885.1|FQ416885
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|351023941|gb|FQ423364.1|FQ423364
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71862284|gb|DT011339.1|DT011339
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGC
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGC
EST: gi|71859164|gb|DT008219.1|DT008219
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|27582878|gb|CB005573.1|CB005573
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|33402557|gb|CF208184.1|CF208184
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|351020144|gb|FQ445751.1|FQ445751
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|351040389|gb|FQ434522.1|FQ434522
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAAG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|352765011|gb|FQ473659.1|FQ473659
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71863774|gb|DT012829.1|DT012829
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCT
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCT
EST: gi|110719282|gb|EE097083.1|EE097083
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAN                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|351025140|gb|FQ433557.1|FQ433557
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71860474|gb|DT009529.1|DT009529
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71860811|gb|DT009866.1|DT009866
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|351036312|gb|FQ458687.1|FQ458687
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71856792|gb|DT005847.1|DT005847
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG
EST: gi|71861673|gb|DT010728.1|DT010728
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTG
EST: gi|110718800|gb|EE096049.1|EE096049
EST:     ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAA                         ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGNGGTTTGCCATANG
genomic: ATGCTAACCAGAGGATGCCTCTCATATATGTCAAACTTTATACATATCAAgtatgtaatg ... gcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG
                                     tgaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatgattttgtttctccaggatttgcatatttttccttttttggtactcctgaccctgatagtaagtgaaaaatgcttaatcagATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC