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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttctttttagccctagttttttccctctctctatgtggattttttgttttcctgtttggtggctgagaaattgaaggaaacgaaaaaaaaaaaattaa...

Basic information

species Vitis vinifera
transcript Vv10s0116g00210.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g39040.1 (Oryza sativa), 5'ss of exon 1
---GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttctttttagccctagttttttccctctctctatgtggattt---tttgttttcctgtttggtggctgagaaattgaaggaaacgaaaaaaaaaaaattaa
       ||  ||   ||  ||||  ||   | |   | | ||  ||| |  || |||||||||||| |  || ||||||||||||||||| ||||||||||||| |  |  || |||    | | |  || ||      |  || |   ||    | ||  |||| ||| |||     |   |    |||  |         |  
CGGACATCAGCCGCGGCCCGTCCGGCTTCCCTGGG--GGCGGCGGCGG-CGGCGGCAGCGACTCCGACGAGCCCCAGGAGTACTACACCGGCGGCGAGAAGAGgtat--tgatacccccgtatatataactttcctcggatcaatctagtttccgctgccgatttgatgg-tgatcgcgtcgtgcgttcgagcactgccgcgctgg

upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G134539_T01 (Zea mays), 5'ss of exon 1
GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttctttttagccctagttttttccctctctctatgtggattttttgttttcctgtttggtggctga-gaaattgaaggaaacgaaaaaaaaaaaattaa--
     |  ||    | | |||  ||     || |    |     |||  || |||||||  ||| |  || ||||| |||||||||||||||||||||||||  | | | |||||   | |       || | | |   ||||   | | ||    ||||   ||    |    |    | | || ||            |  
ACATAAGCCGTGGGCCCGCCGGCTTCCCAGGTGCCGGAGGCGGCGACAGCGGCAGCGACGACGACGAGCCACAGGAATACTACACCGGTGGCGAGAAGAGgta-catctcagcccc--tctcggggacctgtgtttcctgattgactttgttgggatttgcctgcgatcgtgcgtacgagcatcggaatcgccgcttcctagt

upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA15G11860.1 (Glycine max), 5'ss of exon 1
---GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtt-tctttttagccctagttttttccctctctctatgtggattttttgttttcctgtttggt-ggctgagaaattgaaggaaacgaaaaaaaaaaaattaa
   |  | ||||| |||||||||||| |||| |||||  | ||    || ||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| |||| ||  ||| | |    | |   |||     |  || |  || ||      |      ||  |    |      |||| | ||||    ||    
CCGGCAGAATTCGCACCCTCTCCGATCTGAACCGTCCCTCCGCC---GATTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGCGGCGAAAAGAGgttctcttctttcccccaatccaattcaattcttacattctatgtgatgcttcaacactaatccagcccaatcctcatgcaaaaccacaaaattcgaaac--

upper sequence: Vv10s0116g00210.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA09G01010.1 (Glycine max), 5'ss of exon 1
---GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttctttttagccctagttttttccctctctctatgtggattttttgttttcctgttt--ggtggctgag-aaattgaaggaaacg-aaaaaaaaaaaattaa
   |  | ||||| |||||||||||| |||| |||||  | ||    || |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||   || |   | |        ||| | | |       ||  ||  ||   ||| ||    | |      |   | |     | | ||||  | | ||||| 
CCGGCCGAATTCGCACCCTCTCCGATCTGAACCGTCCCTCCGCC---GATTCCGACAGCGACTCCGATGGCCCTCAGGAGTATTACACCGGCGGCGAAAAGAGgttctcttct---cttctccccccccccccccccccccaaatccttaattccactgcttcaaatagtaattcaggctaatcctcatgcaaaaccacataatta-

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|110712280|gb|EE089721.1|EE089721
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110719390|gb|EE097311.1|EE097311
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|161718180|gb|FC066004.1|FC066004
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110691776|gb|EE070262.1|EE070262
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|161721150|gb|FC071025.1|FC071025
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         T--GATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|30251570|gb|CB969303.1|CB969303
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110685329|gb|EE063628.1|EE063628
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|30251625|gb|CB969358.1|CB969358
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|161721790|gb|FC070153.1|FC070153
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110719961|gb|EE095536.1|EE095536
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|29785168|gb|CB341921.2|CB341921
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110384599|gb|EC949049.1|EC949049
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|161718887|gb|FC066370.1|FC066370
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|161713467|gb|FC063098.1|FC063098
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|33403419|gb|CF209046.1|CF209046
EST:     AACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110725917|gb|EE102878.1|EE102878
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110711891|gb|EE088884.1|EE088884
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|30305911|gb|CB982705.1|CB982705
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
EST: gi|110688136|gb|EE066344.1|EE066344
EST:     GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAG                         TGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT
genomic: GACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttcttttt ... acgtctgcagTGGGATGCTTGTCCAAGACCCTTCAAAGGGTAATGATGTGGATGCAATTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCATTCGAACCCTCTCCGATTTGAATCGTCCGACTGCTCCGGACTCCGACAGCGACTCCGATGGCCCTCAGGAGTACTACACCGGTGGCGAGAAGAGgtttctttttagccctagttttttccctctctctatgtggattttttgttttcctgtttggtggctgagaaattgaaggaaacgaaaaaaaaaaaattaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa