Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttacttattctttgtcagtgaaagctgcatcttttctcttcattgcatgcttgaacttaaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG

Basic information

species Vitis vinifera
transcript Vv01s0150g00590.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 5
ttttacttattctttgtcagtgaaagctgcatcttttctct-tcattgcatgcttgaactt----aaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
 | |   |||   |      |||   |   ||||| | | | |  | | ||  |  ||||      |||||||| | |||      | | ||  |   | ||||||| || ||||||||||| ||||| ||||| |||||||||||||||||||||
atatgtgtatggctctctgttgatgtcaatatcttctatgtatggtggtatagtacaactacctgcaaaattcaaggttta-----acaattattccatctgcagGCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAG

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G18440.1 (Glycine max), 3'ss of exon 6
ttttacttattctttgtcagtgaaagctgcatcttttctcttcattgcatgcttgaacttaaaaattcatgttttccgtc-----catattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
  | |||   | ||  | |   | || |  | ||| |||    |     | | | |       ||||   ||| ||  |      ||| |||     || ||||||| || ||||||||||| |||||||||||||||||||| ||||||||||||
-atgactg--tattcataaactagagtt--aacttctcttagaagctggtacatcaggcagctaattttggttatctatggttgacatgtttgtgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGGCTTGAAAAG

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G24350.1 (Glycine max), 3'ss of exon 6
ttttact-tattctt-tgtcagtgaaagctgcatct---tttctcttcattgcatgcttgaacttaaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
  | ||| ||||| | |  ||| |  | || |   |     |   | |||        | |   |    | | ||| |||     ||| |||     || ||||||| || ||||||||||| |||||||||||||||||||| || |||||||||
--tgactgtattcatataccagagttaccttctcttagaagttggtacatcaagcaactaattctggttacttatggtttga---catgtttctgctttatgcagGCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG

upper sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S152_48V6.1 (Physcomitrella patens), 3'ss of exon 6
ttttacttattctttgtcagtgaaagctgcatcttttctct----tcattgcatgcttgaacttaaaaattcatgttttccgt----ccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
        ||| |  ||||      |     | | || | |    | ||       ||| |  |  | |||  |||||    |       | |||||| ||  | ||| | || || |  ||||||||||| |||||||| ||||| ||||||||||||
--------attttaggtcaagtggcgtcttgtttattgtttgctgttatcatggaattgcatatttatatttgtgtttctgataacgttctcttttgtggtgattcagACTGCCATCGCAAATTCACAGACACTTGAAGAAGTTGCCAGGCTTGAAAAG

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|110382187|gb|EC938718.1|EC938718
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
EST: gi|110712685|gb|EE087945.1|EE087945
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTNGAAAA
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAA
EST: gi|110710820|gb|EE087309.1|EE087309
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAAGAACTTATAGCTATCAAA                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGGTGCAAGGCTTGAAAAA
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
EST: gi|110707870|gb|EE084759.1|EE084759
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
EST: gi|32269037|gb|CD718196.1|CD718196
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
EST: gi|110701540|gb|EE079224.1|EE079224
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTTGAAA-
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAA
EST: gi|161714413|gb|FC064424.1|FC064424
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTTGAAA-
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAA
EST: gi|110702872|gb|EE079225.1|EE079225
EST:     AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAG                         GCCGCAATTGTGAATTCACAGACTCTTGAAGAAGTTGCAAGGCTTCGAAA-
genomic: AGATACCAAAAGTGGTGGGCCCTTCACCAGAGGAACTTATAGCTATCAAGgtattatttc ... tgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTT-GAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgcttgaacttaaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG
                                       ttttgtt  CT-rich tract
             ttaaaaattcatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttacttattctttgtcagtgaaagctgcatcttttctcttcattgcatgcttgaacttaaaaattcatgttttccgtccatattttgttgttgtgcagGCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - -ctcttca
- - - - - - - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaat