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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactg-tttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
|||| || ||||| || |||||||||||||||||||||||  | ||||||||  ||||||| ||||| || |||||||||||||| || || || ||||||| |   || | ||   ||   | | || || || ||||    | || |    |||  |||||    ||     | |||| | |                   
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgattctcacttttctcaagatta-gtactagttatctaacttggtacttttgaat-gcag----------------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
|||| || || || ||||||||||||||||||||||| ||| | ||||||||  ||||||| || || || || ||||| ||||| || ||  | ||||||| ||   |||   |   | ||  |  ||| || |  | || ||   ||  | ||| |  |     ||||  |  ||  | ||| ||  |            
CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgt-agc-ctatggatatattcttgtactttttctccctatc-ata--tctgatcttgtagtagtagttaacttcattcttctgt-atgcag-----------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtt--tgtccctttgtctatgactc--------caaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
|||| || |||||||||||||||||||| |||||||| ||||||||||||||||||||||| |||||||| |||||||||||||| ||||| || ||||||| | |  ||| |   |||    ||||||  | |  | |  |   || |||        ||||   | |  || ||| | | |||||| | ||||  |              
CTGTCAAGCATGAACAGAAGCTTGACTGCGGTGGTGGCTACATGAAGTTGCTCAGTGGTGATGTTGATCAGAAGAAATTTGGTGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgttgctctttcctgatgggtgcctctcatatcgcaaaacacctgaccttttaacatttgttgttctgttgcag-------------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctt--------tgtctatgac--tccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
||||||| || |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| ||||||||||| || ||||| || ||||||| | |  ||| |   |||    |||| |  ||  |         || || |||   |  |||     |   | ||| | | |||||| | ||||  |              
CTGTTAAGCACGAACAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGGGATGTTGATCAGAAGAAATTTGGCGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgctgctctttcctgatgggtgcctttgatgttgtaaaacagctgatcttttgacatttgttgttctgttgcag-------------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgt--cagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
| || || || || || ||||||||||| |||||||| ||||||||| | || |||||||| ||||| ||||||||||||||||| || || ||||||||||   | |  ||| |   || ||| ||    | ||    | |     | |   ||| ||        ||||||  |    |    |         |   |||||
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaatt---aacatcaa----tgtttaaaaataacaacccatctgcttttttacctgcag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 3
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctttgtctat---gactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag
|||| || ||||| ||||||||||||||||||||||| |||||||||||||| |||| ||| ||||| || | |||||| || || || || || |||||||  |||||  ||| | ||||| ||  | |    |||     ||    || |||  ||| |  | | ||||  |  ||  |                        
CTGTCAAGCATGAGCAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTAAGTGATGATGTTGACCAGACGAAATTCGGAGGAGACACTCCTTACAGgt--gtgtt--tttcggttact-ttcatatcaaacttcaaacattcaaacaccaggcttatctttctttttttatctgcag------------------------

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|37188532|gb|CF607881.1|CF607881
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110732858|gb|EE108510.1|EE108510
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110372400|gb|EC936562.1|EC936562
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     CAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110700083|gb|EE077719.1|EE077719
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110687770|gb|EE065562.1|EE065562
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110699525|gb|EE076601.1|EE076601
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110732288|gb|EE107443.1|EE107443
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     CAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     CAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|33401998|gb|CF207625.1|CF207625
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|30295872|gb|CB972666.1|CB972666
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATTTGTGGCTATACCCCCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110729565|gb|EE105649.1|EE105649
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110357396|gb|EC920905.1|EC920905
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|294964759|gb|GW838562.1|GW838562
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110702773|gb|EE079035.1|EE079035
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110688081|gb|EE066225.1|EE066225
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110727891|gb|EE105170.1|EE105170
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|30295943|gb|CB972737.1|CB972737
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     TGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: TGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|71870544|gb|DT019599.1|DT019599
EST:     CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     CAAAAGAAATTTGGTGGTGATACCCCATACAG                         CATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC
genomic: CAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgtta ... atgattgcagCATCATGTTTGGACCTGATATCTGTGGCTATACCACCAAAAAGGTCCATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgtcagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG