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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaattagattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA

Basic information

species Vitis vinifera
transcript Vv08s0032g00920.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0032g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G34840.1 (Glycine max), 3'ss of exon 2
----agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaatta-gattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA------
     |||||  | ||  ||   | || |||| ||   | | |   || | | || ||| | || |  | |    | |   ||| ||    | ||     |  |||||   |  |||||||  | || |    |||| | ||||||||||||||| ||||| ||||| ||||| || || |||||||||||||||||||||||||      
gctctgaatg-aacttccat---cagtgtttgctggaaatattatgcactcaagagtatcacttgcaaaatattgcatctgactctgaa-ctgtgaaaaatatagGTTCCAGAAATGGAAG--GCAAGA----CTGAAAGTCATATGACATCAGCAGCAGCCTTTGTGGAAGGGGGGGTTCAAGAAGCTTGTGATGATGCTTGCAGCATAT

upper sequence: Vv08s0032g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G08190.1 (Glycine max), 3'ss of exon 1
agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaattagattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA-----------------------------------------
                               ||| ||  | |  | | |   | ||||    |  |  ||||  ||||||||     |          |||||  ||  |||||||  | || |    || | | ||||||||||||||| ||| | ||||| |||  ||| || |||||||||||||||||||||||||                                         
-------------------------------actcaagagtatcacttgcgaaatatt----gcatctgactctgaactgtgaaaaat--------ataggttccggaaatggaag--gcaaga----ctaaaagtcatatgacatcagCAGCAACCTTTGTGGAA--AGGGGTTCAAGAAGCTTGTGATGATGCTTGCAGCATATGCCTTGAAGATTTTTGCAAAAGTGATCCTGCCACT

upper sequence: Vv08s0032g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G10560.1 (Glycine max), 3'ss of exon 1
---agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaattagattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA------
    |||||  | ||  || || ||| | |    | ||  ||||||    ||| ||| | || |  | |    | |   ||| ||   | |       |  |||||   |  |||||||  | || |    | || | |||| ||||||| || | ||| ||||| ||||| || || |||||||||||||||||||||||||      
ctctgaatg-aacttccat-tggtgtttgttggaaatattatgcact-caagaatatcacttgcaaaatattgcatctgactatgaactatgaaaaaatatagGTTCCAGAAATGGAAG--GCAAGA----CCGAAAGTCATGTGACATCGGCAGAAGCCTTTGTGGAAGGGGGGGTTCAAGAAGCTTGTGATGATGCTTGCAGCATAT

upper sequence: Vv08s0032g00920.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G36270.1 (Glycine max), 3'ss of exon 2
----agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaattagattatt-attttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA---
     || |    ||||  |   |  ||||        || |    |  ||  |  ||| |   | |    ||    ||    ||||||   |  | | | ||| ||||  | |||||||||   || | |    || | ||||||||  |||||||| || ||||||||||| ||  | |||||| | ||||||||||||||||   
aaatggatttccttttgtgttcacaatattgtgcattcaagagcaccccttgcacaattcaaagtattgcatcttactaaggttgtggg--ctgatatgtagAAAGTTGTAGAGATGGAAGA--CAAGACA----GAAAGTCATATGAGTTCAGCTGCGGCCTTTGTTGAAGGGGGGATTCAAGAATCCTGTGATGATGCTTGCAGCA

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|71856366|gb|DT005421.1|DT005421
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
EST: gi|71854963|gb|DT004018.1|DT004018
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
EST: gi|110398157|gb|EC964318.1|EC964318
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
EST: gi|71871792|gb|DT020847.1|DT020847
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGACTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
EST: gi|294964575|gb|GW838378.1|GW838378
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
EST: gi|71856012|gb|DT005067.1|DT005067
EST:     CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAG                         GTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT
genomic: CAATTCCTTCACCCCATTTTCTGGACTGTTTCTGATTTTCCACAATGGAGgtaaacccaa ... tcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA
             ttctgat  putative branch site (score: 3)
                                        ttttgtctttt  putative PPT
     ttattattttctgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatgtgatttggatgtgctgtatttgatgactaaaatgcacaattagattattattttctgatttcgacttagaactgtggggttttgtcttttgaagGTTGAGGGGATGGAAGAGGTAAAAAATTCTGAGAATCATATGACATCAGCTGCAGCTTTTGTTGAAGGAGGAGTGCAAGAAGCTTGTGATGATGCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
-gaatgtg
- - - - - - ggatgtg
- - - - - - - - - - - - - - - -actaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgggg