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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtttatcactggtgtttttataatccagcctcatatcatttacttctcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG

Basic information

species Vitis vinifera
transcript Vv18s0166g00300.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 12
tgattaagaaaaacaagagaccatgcagcccagtcaataact-atgtttatcactggtgtttttataatccagcc-tcatatca----tttacttctcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
                  |   | |||  || ||||    || |   ||  |       |||| ||| | ||    | || |||     |   || | |    |||| || || || || || || ||||| ||||| || ||||| || |||||||| || |||||||||||||||||||| ||||| || ||| |||||||| |
------------------gtataggcatacctgtcagcgtcttaatcttgacctgaacattttcatacttcaatggtaatctcaggcgatcgttttttcatcacagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAAGCGGCACAAACCATGTCCTTCCAACCTATGGTTACGCAAGGATGTATAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 12
tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtttatcac----tggtgtttttataatccagcctcatatcatttacttctc-ctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
   |||    |  |||    || |   |   |    ||   | | |   | |     |||   ||  | |||||    || ||   | |     |  ||||||||||||||||||||||||||  |||||||| || ||||| || ||||||||||| || ||||||||||||||||| || |||||||||||| | ||||||||
---ttataggatccaatt--cctttttgataacctcatttttgtatccttgatggcatggaaattcaagaatcctagatcttaatgtctgtcattggctctgcagGTTCTGTGTTTTTAGGGCCTTGGACACCTGAGAGTGTTGGTGATTATGCAAGCGGGACAAACCATGTCCTTCCTACTTATGGCTATGCAAGAATGTATGG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 11
tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtt-tatcactg-----gtgtttttataatccagcctcatatcatttacttct-cctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
       |          |||| |      || |  |||||    || | ||||        |  ||| | |    ||  | | || |     |  | |||||||||||||||| |||||||||| ||||||||| || || || || |||||||||||||| ||||| ||||| ||||| || ||||| |||||| ||||||||||
-------gctttctccttgacctttactttcatttgataaccgcattctgtcaccacagccataatttcagatggtagatttacatgaccgtttattgcctctgcagGTTCTGTATTTTTAGGGCCGTGGACACCAGAGAGCGTTGGTGATTATGCAAGTGGGACAAATCATGTTCTTCCCACTTATGGTTATGCAAGGATGTATGG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 12
tgattaagaaa-aacaagagaccatgcagcccagtcaataactatgtttatcactggtgtttttataatccagcctcatatcatttacttct-cctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
   ||| ||   ||   |         | | || |    | |  || |      |||   ||  | |||||    || || | | |     | ||||||||||||||||||| |||||||  ||||| || || ||||| || |||||||||||||| ||||||||||||||||| || || || |||||| | ||||||||
cttttaggatccaattcgtttttgataacctcattttgcatccttgatggca--tggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: PP1S15_472V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------------------------------------------------------------tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtttatcactggtgtttttataatccagcctcatatcatttacttctcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
                                                                                                           || |||  | ||   | | ||   ||| |||  | |  ||   |  | ||||   |||||   ||  |  |  ||||||  |||| ||| |     ||||| ||  | ||||| ||    |||||||| || || ||||| || || || |||||||| ||||||||  | |||||||||||||| || |||||||||||
gtgaaatagtaaattttcattactgacagctattcaagttttgagatttaccatgggtgttaaagagaacctgctgcagacatttttctatctgcttggtatcggtgtgcttatcataattgaaatac--ggcaaccccctaatgaagagtaataatca---gtgttggcatggtaaattctcatactattttcttatgtg--gcagGATCCATATTTTTGGGAAGATGGACACCTGAGAGCGTGGGTGACTACGCCAGTGGAACTAACCATGTGTTGCCAACATATGGCTACGCTCGGATGTATGG

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|30251428|gb|CB969161.1|CB969161
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
EST: gi|71885572|gb|DT034627.1|DT034627
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
EST: gi|30126863|gb|CB912202.1|CB912202
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAACTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
EST: gi|351054495|gb|FQ450579.1|FQ450579
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAACTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
EST: gi|71882273|gb|DT031328.1|DT031328
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
EST: gi|71874738|gb|DT023793.1|DT023793
EST:     AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAG                         GTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA
genomic: AATTAATGTGAAAGATGCTGAGAAGTGGGAGAATTTCATTGAGAATGCAGgtacaatttg ... tcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcactggtgtttttataatccagcctcatatcatttacttctcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG
                                  tcatttacttctcctc  CT-rich tract
           tgtttttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattaagaaaaacaagagaccatgcagcccagtcaataactatgtttatcactggtgtttttataatccagcctcatatcatttacttctcctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - -aagaaaa
- - - - - - -caagaga
- - - - - - - - - - ccatgca
- - - - - - - - - - - - - - cccagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - ctggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcctca