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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTATGCCTTCAAAGATCCTATCACAGAATTTTTAGCATGTGTCTATGTCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcctgtacttaatagcggtttaacttcctgatagttccttcagtaaaattttctcactatgtttcccattgaggttcactccaattgagctat...

Basic information

species Vitis vinifera
transcript Vv00s0252g00070.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G33770.1 (Glycine max), 5'ss of exon 5
GCAGTATGCCTTCAAAGATCCTATCACAGAATTTTTAGCATGTGTCTATGTCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcctgtact------------taatagcggtttaacttcctgatagttccttcagtaaaattttctcactatgtttcccattgaggttcact-ccaattgagctat---------------------------------------
|||| || | |  |  || |||||||| || ||||| || ||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||| || || || |            ||  || | | ||||||  || | |||  ||||||     ||| ||  |||  | |   |  | |||  || | |     |  ||                                       
GCAGCATTCATATACGGACCCTATCACTGAGTTTTTGGCTTGTGTTTATGTCAACTATGATTTTGATGGGGCACAAAAGAAGATGAGGGAATGTGAAGAAgtaagcttgctttaatatatgtcaactgtaggagtgatgtaactt--tggtggtttattcagttctcctttatc-ttataatacgtgtccatgttagctactagcactgtaatgggttgtttatattatgcttacctttttaaaatatgcag

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G16090.1 (Glycine max), 5'ss of exon 5
GCAGTATGCCTTCAAAGATCCTATCACAGAATTTTTAGCATGTGTCTATGTCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcctgtacttaatagcggtt----------taacttcctgatagttccttcagtaaaattt--tctcactatgtttcccattgaggttcact-ccaattgagctat--------------------------------------------
|||| || |||  || || || ||||| || ||||| || ||||| ||||| || |||||||| ||||| ||||||||||||||||| ||||||||||||||||| || || || |  ||  |   |          ||      |  | |||  | ||||     ||  ||| |  || | ||   || | |||  || | |    |||                                               
GCAGCATTCCTATAAGGACCCCATCACTGAGTTTTTGGCTTGTGTTTATGTTAACTATGACTTTGATGGGGCACAAAAGAAGATGAGGGAATGTGAAGAAgtaagcttgctttaatatatgtcaactataggagtgatattacttttgtggtttatccagttctcctttatcttataatatatct-gttcatgttagctactagcgtagccccgtaatgggttgtttatattatgcttaccctttttaaaaatgcag

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 5'ss of exon 5
GCAGTATGCCTTCAAAGATCCTATCACAGAATTTTTAGCATGTGTCTATGTCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcctgtacttaatagcggtttaacttcctgatagttccttcagtaaaattttctcactatgtttcccattgaggttcactccaattgagctat
||| ||  ||| ||||||||| || |  || ||  | |||||||| | ||||||||||||||| ||||| || ||||||||||||| ||| |||||||| |||| |   |   |  || |||   |||   ||  ||        | || | || |  ||| ||  | |  |    ||  |                   
GCACTACTCCTACAAAGATCCAATTATCGAGTTCCTGGCATGTGTGTTTGTCAATTATGACTTTGATGGGGCTCAAAAGAAGATGAAAGAGTGTGAAGAGgtaactcatccacatgta-tagatatttttgtttgtgcagaactgtgcaatcaa-tactctgacattttaacatgatgtag-------------------

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|34544009|gb|CF512241.1|CF512241
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|71888199|gb|DT037254.1|DT037254
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110363505|gb|EC927099.1|EC927099
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|351035098|gb|FQ458455.1|FQ458455
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|34543920|gb|CF512152.1|CF512152
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|30302336|gb|CB979130.1|CB979130
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|349827029|gb|FQ421302.1|FQ421302
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATTAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110361713|gb|EC925206.1|EC925206
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|45770682|gb|CN006534.1|CN006534
EST:     TC-ATTATG-CTTCGAT-GAGCAC-AAAGAAGA-GAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110709660|gb|EE085316.1|EE085316
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|30302404|gb|CB979198.1|CB979198
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|351019002|gb|FQ426501.1|FQ426501
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|71883037|gb|DT032092.1|DT032092
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|34544541|gb|CF512773.1|CF512773
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110385422|gb|EC949946.1|EC949946
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110374343|gb|EC939024.1|EC939024
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|110690210|gb|EE067120.1|EE067120
EST:     TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|294967018|gb|GW839893.1|GW839893
EST:     TCAACTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
genomic: TCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTTT
EST: gi|34543854|gb|CF512086.1|CF512086
EST:     AAAAGAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTT
genomic: AAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGAT-CCATTTCTTGGCAAACGTGTTGAAGAAGGAAGCTT
EST: gi|32459206|gb|CD800380.1|CD800380
EST:     GAAGATGAGAGAATGTGAAGAA                         GTAATTTTAAATGATCCATTTTTCTTGGCAAACGTGTTGAAGAAGGAAGCT
genomic: GAAGATGAGAGAATGTGAAGAAgtaagtttcc ... tttaatgtagGTAATTTTAAATGATCCA--TTTCTTGGCAAACGTGTTGAAGAAGGAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTATGCCTTCAAAGATCCTATCACAGAATTTTTAGCATGTGTCTATGTCAATTATGACTTCGATGGAGCACAAAAGAAGATGAGAGAATGTGAAGAAgtaagtttcctgtacttaatagcggtttaacttcctgatagttccttcagtaaaattttctcactatgtttcccattgaggttcactccaattgagctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaaa