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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcccccaccttctttatgcgtaccttgtaaacagaagatttggtcccagtgataaa...

Basic information

species Vitis vinifera
transcript Vv05s0020g04900.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 10
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcccccaccttctttatgcgtaccttgtaaacagaagatttggtcccagt--gataaa--------------------------------------------------------------
||||| | |  |  |||||| ||  |||  |  || || | |||||     | ||| ||||||||||||||||||| |||||||| || ||||||||||||| |   ||    | ||  ||    |   |||  |  |||     |    ||| |   |  ||   |  || |||||    ||||| |    ||   || |                                                               
AATCAGTCATCAGCGCAATGGAATTTGCTGCAAAACAGTTGAACCTCGAATATAAGCTGATGATTAGCAGAGCTTATCATGATTCACTCTTCATGGCCAGgtca---agtactataggccccaacagggttttccacctacaaaccaaataccctggctg-gcaatctctg-aaacatgttatttgctttgtgtctaattatgttctttttgtggggtaacatgtttaccaactaacacgtacaactgcttctttgttctgcag

upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G130034_T02 (Zea mays), 5'ss of exon 10
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagag-aggaagagttcctttgatactttgactgctatgggtcccccaccttctttatgc--gtaccttgtaaacagaagatttggtcccagtgataaa
||||| |     | |||||| ||  |||  |  || || |||||||  |  ||||   ||||||||||||||| ||||| ||||| || ||||||||||||| |   |    |   || ||   || | |  |       || | ||       |  || |  |  | ||  | | |  | || |||   | | |    ||  
AATCAGTCGTTGACGCAATGGAATTTGCTGCAAAACAGTTAAACCTGGCATACAAAAAGATGATTAGCAGAGCCTACCACGATTCACTCTTCATGGCCAGgtgaactactgagcccagctctgatgtttccctttgctgaattgttcttgtttttatttcaaactggaacactatcatta-aatattcctttcaaaaatta--

upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA20G34790.1 (Glycine max), 5'ss of exon 10
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcc-cccaccttctttatgcgtaccttgtaaacagaagattt----ggtcccagtgataaa
|| |||| |  |||||| |  || ||||| |  |||| |||||| |  |   ||||||||||||||| ||||| || ||||||||  |||| ||||||||||||    |||  |||| |     || | || |  |   ||  |          ||| |||||  |  |    |||||     | |      | | | || ||||
AAGCAATCATCAAGGCAGTAGAAACTGCAACAAAAGAACTAAACTTGACAAGCAAGTTGATGATTAGTAGAGCCTATCATGATTCATTGTTTATGGCCAGgtaatctggagagagagat-----gacagttggttttacataagcagatattatttccttatgaattgcccaaaaacattcattcttaaaaattcaaatgttaaa

upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA10G32850.2 (Glycine max), 5'ss of exon 9
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcccccaccttctttatgcgtaccttgtaaacagaag-atttggtcccagtgataaa-
|| || | |  |||||| |  |  ||||| |  |||| |||||| |  |   ||||||||||||||| ||||| || ||||||||  |||| ||||||||||||   ||||  ||||       | |      | |||| |        ||  |  | | | | ||    ||   || ||  |||   ||  |   ||  | 
AAGCAGTCATCAAGGCAGTAGAGACTGCAACAAAAGAACTAAACTTGACAAGCAAGTTGATGATTAGTAGAGCCTATCATGATTCATTGTTTATGGCCAGgtaatctagagagagagagagagaggtgac--aattgcttttacataagcagatattatttccttataaagtgcccaaaaacattcattcttaaaaattcaa

upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 5'ss of exon 10
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcccccaccttctttat--gcgtaccttgtaaacagaagatttggtccca-gtgataaa----
||  | |||  |||  ||||  ||  ||| |   ||| || ||| |||| |||||| ||||||| ||| ||||||| |||||||| || ||||||||||||||  | | ||   |      ||| ||  |  || | |||     |||  | ||| |  ||  | | | | || |  | ||  | ||     ||    ||||     
AACTAGTAATCAAGAAAATGGCAGAGGCAGCCACAGAACTTAACTTATCACACAAGATGATGATCAGCCGAGCTTATCATGATTCTCTCTTCATGGCCAGgtaccacaaagtttgcaag--tttcatcttcagaatacta-----ccctaaacttttaaattagagcatcctgaaccctgataacttttcaacatacaataactatt

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|34364237|gb|CF405822.1|CF405822
EST:     CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
EST: gi|30329287|gb|CD012549.1|CD012549
EST:     CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
EST: gi|110369684|gb|EC933849.1|EC933849
EST:     CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
EST: gi|110377763|gb|EC942850.1|EC942850
EST:     CACAAGTTGATGATCAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
EST: gi|110369681|gb|EC933846.1|EC933846
EST:     CACAAGTTGATGATCAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
EST: gi|110374031|gb|EC938513.1|EC938513
EST:     CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAG                         AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG
genomic: CACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagaga ... ttccttgcagAATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCAATAACAAAGGCAATGCAAGCTGCATCTCAAGAGCTAAACCTATCGCACAAGTTGATGATTAGCAGAGCTTACCATGATTCGCTGTTCATGGCCAGgtaagagagaggaagagttcctttgatactttgactgctatgggtcccccaccttctttatgcgtaccttgtaaacagaagatttggtcccagtgataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagaa