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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta...

Basic information

species Vitis vinifera
transcript Vv04s0008g02100.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G33510.2 (Glycine max), 5'ss of exon 6
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta-
| ||||| || || ||||| || ||  |||| ||| | ||||||| ||| |||||||| |||||||||||||||||||||||| |||| || || ||||||||||||    |  |    | |   |   |  ||   |||  |   |   |   |   |  ||||| ||    | ||  |||||  |  |       | | 
ACAAGGCCCTTGCAAAGGAGCTAAGTGTTAAGGGGCAACTGCACAACATGCATATGAAAGCAGCTCATGGAAAAGCTCAAGAATCTATTTACCGCCAGAGgtttgttgttccccatttctatcactct-tcctatccatgtgacttttggtaaaaatcacaatttgtatgttgtattgttaaaaccagactagacaatgaa

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G06010.1 (Glycine max), 5'ss of exon 5
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta----
|||| || ||||| |||||||| ||   ||||||| | ||||||| ||| ||||||||||| ||||||||||||||||||||| | || || || ||||||||||||    |  |  | | |  ||   |  |    |||  ||  |   |  || | ||  |||  ||  ||| |||| |  |   |           |    
ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGCTGCTCATGGAAAAGCTCAAGAATCCATTTACCGCCAGAGgtttgttgttccccaatgctttcattcc-tgctctccatgtaagtttggat-ataaaaaaagtttatat--gatgttaccaccatattttgctggccccacaac

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA14G12570.1 (Glycine max), 5'ss of exon 5
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccat-ctttttta-----
| ||||| || || ||||| || ||  |||| ||| | ||||||| | | |||||||| ||||| |||||||||||||||||| |||| ||||| ||||||||||||    |  |    | ||| |   |  ||   |||   ||||  ||||  || ||  |     ||| || || | ||||  |  |   |      |     
ACAAGGCCCTTGCAAAGGAGCTAAGTGTTAAGGGGCAACTGCACAACGTGCATATGAAAGCAGCACATGGAAAAGCTCAAGAATCTATTTATCGCCAGAGgtttgttgttccccatttctattgctct-tcctatccatgt--gact--tttg-gtaaaaattccaacttgcatgttgccaaaatgaaacgcacacacacacacat

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G06030.2 (Glycine max), 5'ss of exon 5
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta-----
|||| || ||||| |||||||| ||   ||||||| | ||||||| ||| ||||||||||  ||||||||||||||||||||| | || || |  ||||||||||||    |  | |    ||| ||  |  |    |||  ||  |      || | ||  |||  || | ||  |  |   |  ||  || ||  |       
ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgttcccca-atgctttgattcctgctctccatgtaagtttgga--ataaaaaaagtttatatggcatcatgatgttatcat--attttgctggccccc

upper sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G26280.1 (Arabidopsis thaliana), 5'ss of exon 6
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttg-----ttaactcttacag-atcttgtt------tgg--ttttagt--gatgacagactaatttgtatataatatttggattggattt-tactaaaaatatccatctttttta----------------------------
|||||||  |||| || || || ||  |||| ||  || |||| |  || || |||||||| |||||||| |||||||||||||| || || || ||||||||||     || ||    || | ||||  ||      ||   |||||     |  ||| ||| || | |  ||||       |    | |  |  |   | ||||  ||| || ||                            
ATAAGGCCTTAGCCAAAGAGCTAAGTGTTAAGGGACAGTTGCATAATATGCAAATGAAGGCTGCTCATGGGAAAGCTCAAGAAGCCATTTACCGCCAGAGgtttgacttctttacctgcactgcatctccttgtaacatgatcttttatccgaaacacacactgatatctccataaatgaaaaacaaaactcctgttctcagtatc--tctgttctaacctgcctatgagtaaaaaatgaaacag

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|110382278|gb|EC939049.1|EC939049
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34543212|gb|CF511444.1|CF511444
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|161711452|gb|FC061217.1|FC061217
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|33403975|gb|CF209602.1|CF209602
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACGGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34543102|gb|CF511334.1|CF511334
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34543129|gb|CF511361.1|CF511361
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34542306|gb|CF510538.1|CF510538
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34542224|gb|CF510456.1|CF510456
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|33404062|gb|CF209689.1|CF209689
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACGGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
EST: gi|34543186|gb|CF511418.1|CF511418
EST:     CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAG                         GAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT
genomic: CATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaac ... tgttttacagGAACCCAGTTAGCCCAGAGCTACAGGGAAACGCACGAGGAGAGAGGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata