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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaaaacttcatcttactttttgatttttttttgtccttgaggatgactatggatatcattatggtttcagcatgggcaggttgagcccaaccc...

Basic information

species Vitis vinifera
transcript Vv18s0001g11150.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11150.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os06g11190.1 (Oryza sativa), 5'ss of exon 16
GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatg--tacaaaacttcatcttactttttgatttttttttgtccttgaggatgactatggatatcattatggtttcagcatgggcaggttgagcccaaccc---
| | |  ||  |||||||||||||| |||||||| || || ||||||| |||||| || || ||||| || || |||||||||||||||| ||||    || || |  | | |||     | |  |  |||||||  ||||       ||||  |   | | |   || |  |   | |  || |   | | |    
GGAATAGAAAGGCTTACTTTGAGAGATCACCGATAAACTTCGTTGATAGATTTTCATGTCCAATTATATTGTTTCAAGGATTGGAAGACACGgtaaagctataagatctgaacttctccctcgggtcatttttgt--ttgaatgcagttatgagttctaattt---tttactaccagtatattcaaagctatctata

upper sequence: Vv18s0001g11150.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 5'ss of exon 16
GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaaaacttc-----atcttactttttgatttttttttgtccttgaggatgactatggatatcat--tatggtttcagcatgggcaggttgagcccaaccc
||| ||||| |||||||| |||||| ||||||||||| |||||||| |||||| | || ||  ||||||| || ||||| ||||| || |||||||||  |  | | |     |||     ||||       |  |||   | ||  |     || ||| |||   |  || | | |||| |   ||  |     ||  
GAAATGAAAATGCTTACTATGAGAGATCACCGATCAACTTTGTTGACAAATTTACATGTCCAGTTATTTTGTTTCAAGGCTTGGATGATAAGgtatgtg-atgattgcggaggatcaactattttagacaagtcatgtttgtcagtgtatagttgtataacatgtcaaagtgtta-catgcg---gtgaaaatttac--

upper sequence: Vv18s0001g11150.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA08G42730.1 (Glycine max), 5'ss of exon 16
GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgt-------atgtacaa--aacttcatcttactttttgatttttttttgtccttgaggatg---actatgga--tatcattatggtttcagcatgg-gcaggttgagcccaaccc-------------------------
|| |||| |  |  | || ||| || ||||| ||||||  |||||| ||||||||||| |||||||||||||| ||||||||||| ||||||||       |  | |||  |  ||| | | || | || |||  ||   |  ||   |  ||   | | |  |  |||   ||    | |   ||    | | |  |    || ||                         
GAGGTGAGAAGGGGTGCTATGAAAGATCACCAATCAATCATGTTGACAAATTTTCTTGTCCCATTATTTTATTTCAAGGATTGGATGACAAGgttagcaacaattgcaactattttcctttcacatatttattacttaaaggactctggagtggaaattgtcaacttattcctaaatctactctatattactgataaaaattaatccgataaatatgtcttacacaatgcag

upper sequence: Vv18s0001g11150.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA18G11480.1 (Glycine max), 5'ss of exon 16
GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgta-caaaact----tcatcttactttttgattttttt---ttgtccttgaggatgactatggatatcatta-tggtttcagcatgggcaggttgagcccaaccc
||  ||| |  | |   | ||| || || || ||||||  |||||| || |||||||| ||||| ||| |||| ||||||||||| ||||||||  ||| |||  ||    | || || | ||   || || |    || | |   |   |   |||     |||  | |  | |   ||     |   || ||    |  
GAGATGATAAGGATATGTATGAAAGATCCCCTATCAATCATGTTGACAATTTTTCTTGTCCCATCATTATATTTCAAGGATTGGAGGACAAGgttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcag

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|352777272|gb|FQ473906.1|FQ473906
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
EST: gi|110386770|gb|EC951392.1|EC951392
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
EST: gi|30124740|gb|CB910079.1|CB910079
EST:     TGATAAATTTTCTTGCCCCATTATTTTATTCNCA-GGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAACAA
genomic: TGATAAATTTTCTTGCCCCATTATTTTATTC-CAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
EST: gi|352768447|gb|FQ469623.1|FQ469623
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTTGTAAAATTTACCTGGCACTGAAGAAAAAA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
EST: gi|33406811|gb|CF212438.1|CF212438
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCGATCNATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGA
EST: gi|110359883|gb|EC922159.1|EC922159
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
EST: gi|71884328|gb|DT033383.1|DT033383
EST:     TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAG                         GTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA
genomic: TTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaa ... ttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTGAAAGTGCTTACTTTGAGAGGTCACCGATCAATTTTGTTGATAAATTTTCTTGCCCCATTATTTTATTCCAAGGATTGGAAGACAAGgtatgtacaaaacttcatcttactttttgatttttttttgtccttgaggatgactatggatatcattatggtttcagcatgggcaggttgagcccaaccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacaaaa