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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccctaacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT

Basic information

species Vitis vinifera
transcript Vv09s0002g04000.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 12
gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccctaacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
                 | | || ||| || |    |   ||  ||      |     |||    |  | |||   |   | |    ||||    | || ||| |||||   ||||||||  |||||||||   |||| |  |||||||||||||| ||||||||||||||||||||  | ||| | || ||| | |||
----------------gttagttcttacatacttctttaggtaattgagaaatgcatgttatttca-tatttgt-cgtcatgacactttctctttatagGTTTGGTGTAAGTGGTGCTGATGATGCTGTGAAAAGTTTGAAGTGTATTTGGATTTCCCATATTCATGCTGATCACCACACAGGTGTAGCTAGAGTTCTT

upper sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G379286_T01 (Zea mays), 3'ss of exon 10
gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccctaacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
                 | | || ||  |       || |  ||  | |   | |  ||||     |    ||||  || |  ||| || ||  ||||||||| ||||| | | ||||||  | ||||| |  ||||| || |||||||||||||| ||||||||||||||||||||  | ||  |||| ||||| |||
----------------gttagttcttgcagatcttctagtaatgcataaacctatatattaattacatttatgaa-agtatactgtcttttgt-aacagATTTGGTGTAAATGATGCTGATGAAGCTGTAAAAGGTTTGAGGTGTATTTGGATTTCCCATATTCATGCTGATCACCACACTGGGTTGGCCAGAATTCTT

upper sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G43270.1 (Glycine max), 3'ss of exon 11
----gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccct-aacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
     |  | ||| ||    ||  |||  |   |  | | |||       ||| ||||||  |||   | |||  |||  || |    | |  | ||  ||||||| | ||||    ||||||||  ||||||||||   |||||| || ||||||||||| ||||||||||||||||||||| | ||  |||| || || |||
gtctatccatatccctaac-attcattcatgtttatatagtaccaca--cttaatttctcttttaatatgaactgttggttgat---gtatcctttggaaacagATATGGTGTTACTGGTGCTGATGATGCTGTGAGAACTTTAAGGTGCATTTGGATTTCACATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT

upper sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
----gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccct-aacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
     |  | ||| ||    ||  |||  |   |  | | |||   |   ||| ||||||  |||   | |||  |||  ||||    | |  |  |  ||||||| | ||||    || |||||  ||||||||||   ||| || || ||||||||||||||||||||||||||||||||| | ||  |||| || || |||
gtctatccatatccctaac-attcattcatgtttatatagtaccact--cttaatttctcttttaatatgaactgttggttggt---gtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT

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|77586025|gb|DV222112.1|DV222112
EST:     CTGAAACGAAG                         ATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTG
genomic: CTGAAACGAAGgtaaaaatca ... ctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTG
EST: gi|110375096|gb|EC940053.1|EC940053
EST:     AGTTTGCTCCTAGATTGCGGTGAAGGAACCCTGGGACAACTGAAACGAAG                         ATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTG
genomic: AGTTTGCTCCTAGATTGCGGTGAAGGAACCCTGGGACAACTGAAACGAAGgtaaaaatca ... ctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtttctccattaccctaacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
                 ccctaac  putative branch site (score: 2)
                                  ttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccctaacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA