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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG

Basic information

species Vitis vinifera
transcript Vv00s0204g00220.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0204g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g16530.1 (Oryza sativa), 3'ss of exon 4
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtcctccta----tcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG
                                                                        |||     | |  |   ||  ||  |||  | ||   ||      |  |||     | |   |    ||   || | | || ||     | ||| ||||||||||||   | |||||||| |||||||||||| ||||| | |||||||||||| |    ||||||||   |||  ||
------------------------------------------------------------------------tacttattttgtgaacatgcaattctgtacagtatcagtagtctttgcttccaagaaatacgaggataatgatcttattcttctgacctttaatgtgcagCCAATTGGTCGCTTTCAAGGACAGGCGACAGATGTTGACATAGCAAGAAAAGAAATCCGAAATGTGAAAATAGAAATG

upper sequence: Vv00s0204g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G819807_T01 (Zea mays), 3'ss of exon 4
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG
                                                                   || ||||         |||   |||     | | | |   || | |    | ||  |    |  |  | |||      |||     | | | ||| ||||||||||||   | |||||||||||||| |||||  ||||| |||||||||||||  |    ||||| |||  |||  ||
-----------------------------------------------------------------ctttgtttatggacacacaaaacatgt-gcagtatcactggtatttgcttgctaataatgtgaagctaga-atgtcttaccattgtgacatgt-aatgtgcagCCAATTGGTCGCTTTCAAGGTCAGGCAACAGACGTTGACATTGCAAGAAAAGAGATTCGAAATGTCAAGATAGAAATG

upper sequence: Vv00s0204g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G05440.2 (Glycine max), 3'ss of exon 5
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttac-aaggctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG
                                                                  ||     |  || | |||    |||  |     ||| |||  |||||    |    ||||               ||    ||| | ||   ||||| |||||||||||||||||||||||||||| || |||||| || |||||||||||| |||||| || ||||||||| |||| |||
------------------------------------------------------------------ctagcacatgaatggtcgtttcagttactcttagtttattgtatgtcttttggggatcttttatccaagcttcttaacagtatgccttc---tcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG

upper sequence: Vv00s0204g00220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G15720.1 (Glycine max), 3'ss of exon 4
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaag-tcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG
                                                                 | || | | | ||      ||  ||  | | | |||| |||    |     | || ||  ||  | |||    | || |||  | | ||  | ||||| |||||||||||||||||||||||||||| || |||||| || |||||||||||| |||||| || ||||||||| |||| |||
----------------------------------------------------------------ttgttgtgtgctagcacatgaatggtcgcttca-gttacttagtcttttggggatcttttatccaagtttc---ttaacagtagtatgctttt-tcaatttgcagCCAATTGCAAGGTTTCAAGGTCAAGCAACAGATGTTAACCTTGCAAGAAGAGAAGTCAATAATGTGAAGACAGAATTG

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|26263712|gb|CA814775.1|CA814775
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTG
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTG
EST: gi|349817360|gb|FQ405364.1|FQ405364
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|352786866|gb|FQ481241.1|FQ481241
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349818802|gb|FQ409336.1|FQ409336
EST:     CCAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|351033443|gb|FQ462094.1|FQ462094
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|110685889|gb|EE063005.1|EE063005
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349815211|gb|FQ400366.1|FQ400366
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349812676|gb|FQ409835.1|FQ409835
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349816081|gb|FQ399312.1|FQ399312
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349810618|gb|FQ402861.1|FQ402861
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349817965|gb|FQ407954.1|FQ407954
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349820386|gb|FQ406942.1|FQ406942
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|352786251|gb|FQ478862.1|FQ478862
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|349819431|gb|FQ412325.1|FQ412325
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAGTTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|26265704|gb|CA816767.1|CA816767
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTG
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTG
EST: gi|351051760|gb|FQ449574.1|FQ449574
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAA-C--                         C-AATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
EST: gi|110713345|gb|EE089186.1|EE089186
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAAGTTTCAAGGTCAAGCGACAAATATTGACCTTGC
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGC
EST: gi|351024251|gb|FQ423674.1|FQ423674
EST:     CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAG                         CCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA
genomic: CAAAGGGAAACCGTTCAGCTTTGCCTTCATCAACAATCATGATAAAGCAGgtttcttctt ... caatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG
                ttttaac  putative branch site (score: 2)
                                    tcctcctatc  putative PPT
               attttaacatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttcttgactagtactttttattgctctaagctactgcgtatctgttgttctcttgctttgtcttttttacaaggctcgaaagagtgtcatgatgttaattaaatgtccaaagtcattcttcagattttaacatgaaaagtcatgtcctcctatcaatctgcagCCAATTGCAAGGTTTCAAGGTCAGGCGACAGATATTGACCTTGCAAGAAAAGAAGTGAAGAATGTGAAGGCAGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA