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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattactgagctaaaagaccagctttgggcaaccgattctttatcattactgtgctttgggttgaaattgtacaagagattgatcttctaggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT

Basic information

species Vitis vinifera
transcript Vv02s0025g00270.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------aattactgagcta--aaagaccagctttgggcaaccgattctttatcattactgtgctttgggt---tgaaattgtacaagagattgatcttctaggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
                                                                              |   |  |     | |      |||    | | | ||  || | | | ||  |   |||  |   ||   |  ||      | |||  |  |  |  ||||||||||| ||||| ||| || | |||||  |||||||||| ||||| ||||||||||||||||||||||| ||||| ||||||||| | || ||||||||||
gtttgttgcttccagcttgtgctttgctgaaacattttgcttgcagaaaatctagacagagatttccatgcaccttgttcctttggtcgctatatgttttcttcatcctatccatatttcagcttaacattctcttgtttatctggtttaataatcacaagtgacatgttttgcattgcagTACTTCCTGTACCAGTTGCTACGAGGGCTAAAATATGTGCACTCGGCAAATGTCTTGCACCGTGATCTGAAGCCAAGCAATTTGTTCCTTAATGCAAATT

upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
-------------------aattactgagctaaaagaccagctt-tgggcaaccgattc---tttatcatta-----ctgtgctttgggttgaaattgtacaagagattgatcttctaggattt-gcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
                     || |||   ||||  | |   |  |   | | | ||||   |  | || ||     ||||   ||   |    ||| ||  | |      |||| |    ||| |||||| ||||| |||||| |  | |||||||| || ||||| || || ||||||||||||||| | || || | ||| || |||||||| |||||||| || |
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT

upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
aattactgagctaaaagaccagctttgggcaaccgattcttta--tcattactgtgctttgggttgaaat-tgtacaagagattgatcttctaggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
    |  || ||| |      |    | |  |   ||   ||   |||  ||  || | |    |  ||| | ||        |   |   |     |||||||||||  |||||||| |||| |||||  |||||||||| ||||| |||||| | |||||||| ||||| ||||| ||||||||| | || ||||||||||
--acaaagaactatatt-ttggtacggagggagtaatatattgcttcacaacaatgatatattctataatctatatttctatgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT

upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------aattactgagctaaa--agaccagctttgggca-accgattctttatca-----ttact-gtgctttgggtt-gaaattgtacaagagattgatcttctagga----tttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT---------------
                                                          | ||    |   | |  |  ||  |||   ||| |  |  | || || |     | ||| |||||||   || ||||||   || |  ||  || ||    ||    | ||||||||||| | ||||||||||| || ||  | |||||||| || ||||| ||| |||||||||||||||| |||||||||||||||||||| |||||||| |               
gtcaggtttccttctatttatattatttcgttttcagttttctattcatattctatacagttttgtattcagattattccttcttattgcataagggctgttaattaagttttgacttgtgcttttcttttgaaattaagcatggtatccatgtttcgtgaaacttgtgcagtactttttatatcagCTGTTACGGGGGCTGAAATATGTGCATTCTGCTAATATCTTGCACCGTGATCTTAAGCCCAGCAATTTGCTTCTCAATGCAAACTGTGACCTTAAAATTG

upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------aattactgagctaaa---agaccagctttgggcaaccgattctttatcattactgtgct---ttgggttgaaattgtacaagagattgatcttctagga----tttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
                                                                    |||   |||  || |   |  |    |    |       || || |   ||  | || |   ||   ||||||||   |  |  |||||| ||    ||    | ||||||||||| | ||||||||||| || ||  | |||||||| || ||||| ||| |||||||||||||||| |||||||| ||||||||||| ||| |||| |
gtttccttctattcatattctatacagaaaaaaatctttcaagcgattaaatcgacacatgtattttaaatatatgaaatagattcattcttattgcatgaggggtgttgttaagttttgatttgttcttttcttttgaaattaagcttggtattgatgtttcgtgaaacttgtgcagTACTTTTTATATCAGCTGTTACGGGGGCTGAAATATGTGCATTCTGCTAATATCTTGCACCGTGATCTTAAGCCCAGTAATTTGCTTCTCAATTCAAACT

upper sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S59_325V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------aattactgagctaaaagaccagctttgggcaaccgatt--ctttatcattactgtgctttgggttgaaattgtacaa--gagattgatcttctaggatt-----tgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
                           ||  |    |      | | | ||       |||||  ||| |  | |  |||  ||   |||||  |    ||   ||| ||||  | ||  | |      ||||||||||| |||| |||||  | || ||  | || ||  | ||||| || || ||  | ||||||||| ||||||| |||||||||||||||||||||||||
gtgtgactgattgattttttttttttttttttttttttttttgctaccgtttcttcgtcgattttcttcactactgttgtttttcttgttgatgtgtggcagtggagtttgagatactgtgttactttgtgcagTACTTTTTGTACCAGCTACTTCGTGGGCTCAAGTACATTCACTCGGCGAAAGTTCTTCACCGTGATTTAAAGCCGAGCAATTTGCTTCTGAATGCAAATT

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|71857199|gb|DT006254.1|DT006254
EST:     TTCATCAGATCATTTGTTCTAACCAATCCCTCACCGATGATCATTGTCAG                         TACTTTCTGTATCAGCTGTTGCGAGGATTAA
genomic: TTCATCAGATCATTTGTTCTAACCAATCCCTCACCGATGATCATTGTCAGgtatctcact ... ggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAA
EST: gi|71889081|gb|DT038136.1|DT038136
EST:     TTCATCAGATCATTTGTTCTAACCAATCCCTCACCGATGATCATTGTCAG                         TACTTTCTGTATCAACTGTTGCGAGGATTAAAATATGTACACTCTGCAAAT
genomic: TTCATCAGATCATTTGTTCTAACCAATCCCTCACCGATGATCATTGTCAGgtatctcact ... ggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactgtgctttgggttgaaattgtacaagagattgatcttctaggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT
                                gattgat  putative branch site (score: 4)
                ttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattactgagctaaaagaccagctttgggcaaccgattctttatcattactgtgctttgggttgaaattgtacaagagattgatcttctaggatttgcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT

- - - - - - -aaagacc
- - - - - - - - - - - - - - - - - - - - - - - - actgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagaga