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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta...

Basic information

species Vitis vinifera
transcript Vv16s0100g00640.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G29570.1 (Glycine max), 5'ss of exon 2
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta-
 |||||||||| ||||||||||||||  | |||||| |||| |  || ||||||||  ||||||| ||||| ||||| || ||||||||||| || ||| ||||||  ||||       |     | |  || | |   |||   ||||   ||    |         |||   | |      ||     ||   ||  | 
TTCACTTGCATTTGGTTACATGCTGGGGTTATTCATTTGCTAGCTAATATGTTGAGTCTGGTCTTCATTGGCATTCGCCTTGAACAGCAATTCGGATTTAgtatgtttttcttccaaactagtaatatcttcttacga-ttacattgatggcacgtagtaaatgtcacacaaaataaggaaaacaaatattaaacttccaa

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G32150.1 (Glycine max), 5'ss of exon 2
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtg--gttctcttgcttttagtgtgttgtcattcaccttagg-------------ctgatccgactcccttgcctctggacattgttatcttcccat------tccatatcatttta--------------------------------------------------------
||||||||||| ||| | || |||||  |  ||||| ||  ||  |||||||||||| ||||||| ||||| ||||| || ||||| |||||||| ||||||||||    || |  ||||| |     ||| |     |  |||||             |   |   | |    | ||| ||||||| || | |             | ||| |  ||||                                                         
GTCACTTGCATTTGGCTGCACGCTGGAGTTGTTCATTTGGCTGCCAACATGTTGAGCCTGGTCTTCATTGGCATTCGTCTTGAACAACAATTTGGGTTTGgtatgtttcttttttctgcttatttcaggttatacacaaaattaggaaataaaaaaattcaagttttagttttatacctttggacatggtcaccccatttggaagtgttcatgttcttttgtgttcttcaaattttgcttttgaatggttatgacctgacatttttcaaaacggcag

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G38290.1 (Glycine max), 5'ss of exon 2
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta-
||||||||||| ||||||||||||||  | |||||| |||| |  || ||||||||  ||||||| ||||| ||||| || ||||| ||||| || ||| ||||||  ||||       | |||    | |  ||    |||   ||||   ||    |         |||   | |      || ||  ||  | |  | 
GTCACTTGCATTTGGTTACATGCTGGGGTTATTCATTTGCTGGCTAATATGTTGAGTCTGGTCTTCATTGGCATTCGCCTTGAACAACAATTCGGGTTTAgtatgtttttcttccaaact-agtaaaatctgcttatggttacattgatgtcacgtagtaaatgtcacacaaaataagtaaaacaatcattaaaaatccaa

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G26610.1 (Glycine max), 5'ss of exon 2
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta-----
||||||||||| ||||| ||||||||  |  ||||| |   ||  |||||||||||  ||||||| ||||| ||||| || ||||| |||||||| ||||||||||  |||| ||   |   |  | ||     | |  | | ||   |||   |    ||  | |  |||     |  |    | |  | | ||||  |     
GTCACTTGCATTTGGTTGCATGCTGGAGTTGTTCATTTAGCTGCCAACATGTTGAGTCTGGTCTTCATTGGCATTCGCCTTGAACAACAATTTGGGTTTGgtatgt--ttcttttatct---gcttatttcaggttatttgaagcaattccatttagtgtgaatttatacacccgaagttaggaaataaaaaacattcaagtttt

upper sequence: Vv16s0100g00640.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 5'ss of exon 2
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta
 | || || || |||||||| || ||| | ||||||||    |  || ||||| ||| | || || ||||||||||| ||||| |||||||||||||||||||||   ||    ||  |||||| | |  |  |||   ||  | |  || |  | |      |||| |  ||| | ||||   |||             
TTGACATGTATATGGTTACACGCGGGTGTTATTCATCTCGGAGCCAATATGTTAAGCCTTGTTTTCATTGGTATTCGTCTCGAGCAGCAATTTGGTTTTGgtatgcaatttgggtggatttagtct-tcattcttctagttgtgttattctg-ttgctagaaatctgaatcttggtttcttgaaattttcag--------

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|351035890|gb|FQ463735.1|FQ463735
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351055680|gb|FQ452145.1|FQ452145
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351034814|gb|FQ458171.1|FQ458171
EST:     GTTGAGCTTGGTCTTGATTGGTATTCAACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAAT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAAT
EST: gi|351047313|gb|FQ451825.1|FQ451825
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|349814964|gb|FQ410187.1|FQ410187
EST:     ATTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|161718477|gb|FC065046.1|FC065046
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|349821089|gb|FQ404342.1|FQ404342
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351016253|gb|FQ446113.1|FQ446113
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAATAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351041883|gb|FQ456093.1|FQ456093
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|352789912|gb|FQ478727.1|FQ478727
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351048431|gb|FQ448705.1|FQ448705
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGTTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAAGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351035144|gb|FQ458501.1|FQ458501
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
EST: gi|351055425|gb|FQ442023.1|FQ442023
EST:     GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTG                         TGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT
genomic: GTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggtt ... gttttggcagTGCGGATAGGAGTAATTTACCTGTTGTCAGGATTTGGAGGGAGTGTTCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTGCATCTGGTTACATGCTGGTATCATTCATCTGCTTGTAAACATGTTGAGCTTGGTCTTGATTGGTATTCGACTCGAACAGCAATTTGGTTTTGgtatgtggttctcttgcttttagtgtgttgtcattcaccttaggctgatccgactcccttgcctctggacattgttatcttcccattccatatcatttta

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttccc