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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG

Basic information

species Vitis vinifera
transcript Vv03s0038g04250.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 11
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
      || |      |   ||   | |||  | | ||| ||   | ||||    |||  |||    |  |  |||  |       ||  || | | ||| | || ||||||||||| ||  ||||||||||||||||||| || ||||| ||||| |||||||| ||||| || || |||||||| ||  |  ||||||
-----gtaagaaacctagacctgattataaactga-tggttaatcaattgaagacgttcctctc---acctgtaaatca-------tgtattct-tgcagATTGGCTGGATCTATGGTTCAATTACAGAAGATATCTTGACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCTATTTACTGCATTCCAAAGCGGCCAG

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 8
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcat-tgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
           |  | | ||   |||| |  | |  |  ||   || |||||           | | |||||  |||||  |   | |  ||||  | ||| | || |||||||| ||||| ||||||||||||||  | || |||||||| ||||| |||||||| ||||| || || |||||||| ||| |    || |
----------gtaaggactggagcctg-attgctgttaactggttaattgattg---------aaacatttcttaactagttaattatatctttgttgcagATTGGCTGGATCTACGGATCAGTTACAGAAGATATTCTAACTGGTTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACTACCTG

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 12
tttttctaggttttgcattgctccctgtaaggttactggctat--ctatttgatcctgtttttctag-aaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG----------------------
                   |     | ||  | |  ||| |||  || | |||  |      | |   | ||    || |  |  ||||  | |  | ||||| | || |||||||||||||| ||||||||||||||  | || ||||| || |||||||| ||||| ||||| || || |||||||| ||| |  ||   |                      
-------------------gtgaagtctagagcttgtggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcat--cttacttttcagattggctggatctatggatcagTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTGCATTCAAAGGTTCTGCACCTCT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 12
tttttctaggttttgcattgctccctgtaaggttactggctat--ctatttgatcctgtttttctag-aaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
                   |     | ||  | |  ||| |||  || | |||  |      | |   | ||    || |  |  ||||  | |  | ||||| | || |||||||||||||| ||||||||||||||  | || ||||| || |||||||| ||||| ||||| || || |||||||| ||| |  ||   |
-------------------gtgaagtctagagcttgtggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcat--cttacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 10
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
    ||||  |     ||  |       ||    ||| || |   | |  |       | | | | | |    | || |    |  | ||||   | ||| | || ||||| || |||||  | ||||| ||||||||||| || ||||| ||||| |||||||| ||||| || || |||||||||||  |  |||| |
---gtctatataccatataacctgactcaaaag-acttgcgactaactctactagagatgtattgtactaagtagacca---ccggttccttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAGATGCACTGCCATGGCTGGCGGTCTATTTACTGCATCCCGAAGCGGCCTG

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 12
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
         ||   |  |||  ||   |  ||||| ||| |    | |  |  |   | ||  | |       || |  |    |||  | |||  |||| | || |||||||||||||| |||||||| |||||  | || ||||| || |||||||| ||||| ||||| || || |||||||| ||| |  |||| |
---------gtaaagtcttgagcc---tgtggttattggttgatgagtcaaaacatatgttacatag----tgaatcatatgatattttccttt--tcagATTGGCTGGATCTATGGATCAGTTACAGAGGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGCCTG

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 12
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcat--tgccttttatt-cagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGA-CAGGCCAG
      || || | ||||  |    |||    ||  ||  |||   ||  | | ||| |      ||   | |  ||  |||  ||  | | |||| || ||| | |||||||| |||||||| || |||||||||||  | || || ||||| ||||| |||||||| ||||| || || |||||||| ||| | | ||||  
-----gtaagtgt-gcatcacgttttgttgtatt--tgcatattggttgcaacgtgtatggtcgaaataattatcacatactaaatcatacgttttgttacagATTGGTTGGATTTATGGATCAGTCACAGAAGATATTCTTACTGGGTTTAAGATGCACTGCCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGCCG-

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|161714301|gb|FC064180.1|FC064180
EST:     TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAG                         GTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
genomic: TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg ... ttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
EST: gi|30304878|gb|CB981672.1|CB981672
EST:     TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAG                         GTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
genomic: TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg ... ttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
EST: gi|71860009|gb|DT009064.1|DT009064
EST:     TCCATGTGATTAGCTGTGGTTATGAAGATAAAACAGACTGGGGAAAAGAG                         GTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
genomic: TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg ... ttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
EST: gi|110727924|gb|EE105243.1|EE105243
EST:     TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAG                         GTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
genomic: TCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg ... ttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
EST: gi|33407928|gb|CF213555.1|CF213555
EST:     GTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAG                         GTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA
genomic: GTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg ... ttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG
                             aactaac  putative branch site (score: 1)
                                   cttcattgcctttt  CT-rich tract
           tttttctagaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctaggttttgcattgctccctgtaaggttactggctatctatttgatcctgtttttctagaaatttcaaaactaacttcattgccttttattcagGTGGGTTGGATCTATGGATCTGTTACAGAAGATATCTTGACAGGTTTTAAAATGCATTGCCATGGATGGCGATCCATATACTGCATCCCTGACAGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - ttttgca
- - - - - - - - - tgctccc
- - - - - - - - - - - - - - - - ttactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgcc