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

CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag

Basic information

species Vitis vinifera
transcript Vv08s0105g00430.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os07g49310.2 (Oryza sativa), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| || || || ||    ||| ||| |||  | |  ||||| ||||||||||| || ||||| |||||||||||||| ||||| || || ||||| ||||||||       | ||  |  | || |   ||      | || |   |  ||      | ||  |  ||||   ||    ||| |  | |                                   
CTGCCGCCGCCGCGCGCCTCCACAGCTGCCTCGCCTGGCCGCTCTACTGGGCGGCGCAGGGAACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacgacggtattcatttccattttgattcctactccactctactacactag----tagtaattaattcgttcatggaattggaattgcag--------------------------------

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| || || || ||     || ||| |||| | || ||||| ||||||||||| || ||||| |||||||||||||| ||||| || || || || ||||||||  | | |   |||  || |      |  ||| | | |  ||   | ||  |||| |   |     ||   | |        ||  || | ||  |  ||| ||||               
CCGCCGCCGCCGCGCGCGTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTGCTGGGTCACGACTGgtacgccc-ctgcctccatcctagagattggatttttttttcttttctgtgggttttagcttttgcagcccggatcgttgacccttccttccctactcggtgtctttgcag------------

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G128971_T01 (Zea mays), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtt--tcagtctgtattttgg--tgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| || ||||| ||    ||| ||| |||| | || ||||| ||||||||||| || ||||| |||||||||||||| ||||| || || ||||| ||||||||  |   ||  |     ||  |  |  |  | | |    ||    | ||| | |||||   || | | |||   ||  ||| || || ||  |   |  | |  ||  |   |    | ||||||
CCGCAGCGGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaggcctccagcc-----ctccacggtcccgtgcccaacattggatactcttttttttgtcctgttattttcattcatgccagtt-ttaggcctttgactcctgctgcatatctgctgt-ttgcag

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| ||||| || ||    ||| ||| |||| | || ||||| ||||||||||| || ||||| |||||||||||||| ||||| || || ||||| ||||||||  | | |||| |   |||  || |  || || |   |||||      | |  || |  ||||  ||          ||||  | ||  |  |||  |  ||||||               
CCGCGGCCGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacgcac-caatgt---tctggattgccctgttgt---tgtttttcatggaagctttggactctggtc----------tttgacttgtgccgcatgtctgctgtttgcag------------

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA03G07570.1 (Glycine max), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag-----------------------------------------
| || || || |||||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||  | |||| ||  | || |||  || ||  | | |  ||   | | | | ||  |  | ||   | | |  | ||| || | | ||    |     ||| |  | || ||| |   |                                          
CTGCTGCTGCAGCTTATCTCAACAATTGGGTTGTTTGGCCTCTCTATTGGGCTGCTCAGGGAACCATGTTCTGGGCCCTCTTTGTTCTTGGTCATGATTGgtaattgc-caatttca-tattgatatctccatgtttttttattttttatttttattactaatgtagatctagattcaatt-gtatagattggcttttggggtggtaaagttggatttcaaaagtttgttatgataaccatggttggtgttttggatgtttcag

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G29630.2 (Glycine max), 5'ss of exon 2
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaat-------ctcacaat-----ctctctcttt---------atagatctattctct-ctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgat---tttgatgttgcag
| |  || || |||||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||        ||| | |     |||  |||||          ||||||||   ||   ||| |   |  |  |||||| |   ||       |   ||   ||||| | | ||    |   || ||| |   || |||||| |||
CTGTTGCTGCAGCTTATCTCAACAATTGGGTTGTTTGGCCTCTCTATTGGGCTGCTCAGGGAACCATGTTCTGGGCCCTCTTTGTTCTTGGACATGATTGgtaatagtcaatttcatattgattactccatcttttttactaatgtagatctagattcaattgtatagattggctttttggggtggtaaagttggatttcaaaagtttgttatgatgataaccatggttggtgttttggatgtttcag

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G18350.1 (Glycine max), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctc-----acaatctctctctttatagatctattctc-tctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
|  | || || ||||||||||| || ||| | |||||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| ||||| ||||| |  |     || || | ||| ||  |   | | ||    | ||  |    ||||||||||| |  |            | |    | ||  || ||  |  |  |  ||| |||   |||| |||
CTTCTGCTGCTGCTTATCTCAATAATTGGTTGGTTTGGCCTCTCTATTGGGCTGCTCAAGGCACTATGTTCTGGGCTCTGTTTGTTCTTGGTCATGATTGgtactaactaataactatttttcttttcttcattatgttaaaatttggatgtagctgtattttggagtgcagaattgggtttcaaaaactgtgacttgatgggtttgtttgttgttttgtgtgtttcag

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA18G43210.1 (Glycine max), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatc-tcacaatctctctctttatagatctattct--ctctgtttcagtc---tgtattttggtgctctattccaacacc-ccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
  || || || || |||||||| || ||| | |||||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| ||||| ||||| |  | || || | ||| ||  |   | | || |   |  | |  ||     || | |   |   |   || ||| |     | |||||  ||||  |     || ||| || |||   |       
-TGCTGCTGCTGCGTATCTCAATAATTGGTTGGTTTGGCCTCTCTATTGGGCTGCTCAAGGCACTATGTTCTGGGCTCTGTTTGTTCTTGGTCATGATTGGtactaataactatttttcttttcttcattttgttataatttggatgtagctagatggagtgcagaattgggtttcaaaattgtgacttgttgagtttacttgttgttttgtgtg-tttcagt-------

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EDP09401 (Chlamydomonas reinhardtii), 5'ss of exon 4
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaa----tctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag-------------
                            |    | ||||| || ||||||| ||||||||| |||||||||||||| || |||||  | ||||| ||||||| |    ||   ||     | |   |  |  ||| | ||| ||||  | |    |   ||||   |      | |||||   |  ||   |  ||      ||  |    |    |    ||||               
----------------------------GTGGATGTGGCCCCTGTACTGGGTTGCTCAGGGTACCATGTTCTGGGCTCTGTTTGTGGTCGGCCACGACTGgtgagtggtcctgcacataatgtggcttcatgtctgtcctcactgtaccggc---tgagttggcctttcccgtcgacaccatgta-gtgcagactccagcaaatcattaacgccccttcacttgccttttgcccacacag

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtct-gtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| || |  || |||||  | || || ||| | || ||||| |||||||||||||| || ||||| ||||||||||| |||||||| || |||||||||||||||  |     | |||      | | |  | || |  || | ||  |||      |   || ||                                                           
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtt-----tttcttctcccaaaaacttgtttttgctttctcgttcttacgcgtctttgatcag---------------------------------------------------------

upper sequence: Vv08s0105g00430.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ20170 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtct-gtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag
| || |  || |||||  | || || ||| | || ||||| |||||||||||||| || || || ||||||||||| |||||||| || |||||||||||||||  |     | ||||||     |    | || | ||| | ||  |||      |   || ||                                                           
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGCACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgtaagtt-----tttctctcccagcaa---tgttttttctttctcgatcttacgcgtctttgatcag---------------------------------------------------------

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|351026647|gb|FQ436300.1|FQ436300
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|33404634|gb|CF210261.1|CF210261
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACATGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|351044129|gb|FQ452802.1|FQ452802
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCAACAATCTCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|33410242|gb|CF215869.1|CF215869
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|351036570|gb|FQ457283.1|FQ457283
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|71862276|gb|DT011331.1|DT011331
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACATGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|349820121|gb|FQ404843.1|FQ404843
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCGACAATCCCAAGCTAAACAGTGTGGTCAGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA
EST: gi|349820954|gb|FQ408662.1|FQ408662
EST:     GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTG                         TGGACACGGAAGTTTTTCCAACAATCCCAAGCTAAACAGTGTGGTCGGGCA
genomic: GCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcac ... gatgttgcagTGGACATGGAAGTTTTTCCAACAATCCCACGCTAAACAGTGTGGTCGGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGGCGGCGGCTTATCTCAACAACTGGGTTGTTTGGCCTCTCTACTGGGCTGCTCAGGGGACCATGTTCTGGGCCCTCTTTGTTCTTGGCCATGACTGgtaatctcacaatctctctctttatagatctattctctctgtttcagtctgtattttggtgctctattccaacaccccatttgtttggtttcatatgcattgtgtttgattttgatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT