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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttttttgagttaaaatgttactttgccataacatctttgtgtctcgtcatctatgttacatggacttgggtacaagtattgggtgttgatgtgc...

Basic information

species Vitis vinifera
transcript Vv00s0360g00050.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttttttgagttaaaatgttactttgccataacatctttgtgtctcgtcatctatgttacatggacttgggtacaagtattgggtgttgatgtgc
|||  |  |||||||  | || ||||||||||| || |||||    |||||||| || ||||| || |||||||||||||| || |||||||||||  | |||||        ||||  | | ||  ||| ||      |  || ||| | ||  |||       |     |    | ||| |    |            
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagc-------agttctattattggtttcccggctatttattctgtattgttttcttcacccaactctgtgacttgcaattcccag------------

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA08G46170.2 (Glycine max), 5'ss of exon 9
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt--ttgagttaaaatgttactttgccataacatctttgtgtctcgtcatctatgtta-catggacttgggtacaagtattgggtgttgatgtgc
||| ||| ||||||| |||||||||||||||||||| ||||| | ||  || ||||| |||||||||||||||||||| ||||| ||||| ||||||||||| ||| ||    ||  ||   | |  ||||     |  ||||||    |   ||    ||   |  ||    ||    |     | |    | ||  | |  
TCCGCATTTGATTGCTTTAGCTTGCATATACATTGCTAGTGTGCTCAGGGAGAAAGACACCACTGCTTGGTTTGAAGAACTTCGTGTTGATATGAATGTGgtgagtattccactgtatttctaagc-acttgtttgttgcatcttaa-attaagtttcttacactgtcactttctcctctctctctctctcttttttttttc-

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA18G33140.1 (Glycine max), 5'ss of exon 8
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttt----tttgagttaaaatgttactttgccataacatct-ttgtgtctcgtcatctatgttacatggacttgggtacaagtattgggtgttgatgtgc
 || ||| ||||||| |||||||||||||||||||| ||||| | ||  || ||||| |||||||||||||||||||| ||||| ||||| ||||| ||||| ||| ||    | |   |  ||    |  ||||  ||| | ||  ||  || || |   || |           ||   |      |||   |  |       
-CCGCATTTGATTGCTTTAGCTTGCATATACATTGCTAGTGTGCTCAGGGAGAAAGACACCACTGCTTGGTTTGAAGAACTTCGTGTTGATATGAACGTGGtgagtattccactgtatttctaagcacttgtttgttatatcttcaattaggtatcttagcctgttactttctctttttttttttcccatttacttctttc----

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT5G48640.1 (Arabidopsis thaliana), 5'ss of exon 8
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttttttgagttaaaatgttactttgccataacatctttgtgtctcgtcatc-tatgttacatggacttgggtacaagt-attgggtgttgatgtgc----------------------
|||  | |  || ||  |||| ||||||||||| |||||||| |||| ||| ||||| | |||||| ||||||||||| ||||  |  ||||||||  |||| |||  || |   |  ||| |||| |    ||| |  |    | |  | |  ||  | | || | ||   || ||||    | | ||  | |  | |  |                      
TCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAGAAAGATATCACTGCATGGTTTGAAGATCTTCATGAGGACATGAACTTGgtcagtcattct---tctaaaagttattcaatcatta-gttaaagcgaatagctatgatcttttgcgtgattttcggtattctttagtgactttgaaagctctacatggggcaatgggttgcag

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|110421670|gb|EC987970.1|EC987970
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCAATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|110695053|gb|EE072630.1|EE072630
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|110709326|gb|EE084688.1|EE084688
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCAATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|110364321|gb|EC923868.1|EC923868
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|161719540|gb|FC067026.1|FC067026
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGA-CG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|110730965|gb|EE108649.1|EE108649
EST:     TAAAGAAACCACTGCNTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCAATGGAGATACTAGATTTCTATGACAGCCACA
genomic: TAAAGAAACCACTGC-TTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACA
EST: gi|77582414|gb|DV220179.1|DV220179
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|110713415|gb|EE089326.1|EE089326
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAA-TATCTCAATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|32247896|gb|CD713715.1|CD713715
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGAACG
EST: gi|349814319|gb|FQ398759.1|FQ398759
EST:     ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTG                         GTAAAAAATATCTCAATGGAGATACTAGATTTCTATGACAGCCACAGA
genomic: ATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagttttt ... actttgacagGTAAAAAATATCTCCATGGAGATACTAGATTTCTATGACAGCCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttttttgagttaaaatgttactttgccataacatctttgtgtctcgtcatctatgttacatggacttgggtacaagtattgggtgttgatgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT