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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt...

Basic information

species Vitis vinifera
transcript Vv08s0040g00430.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataac-ttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt-----
|||| |||||||||||||| || || |||||||| || || ||||| ||||||||||||||||| || ||||| || || ||||| || |||||| |   |     || |  | ||||||| |     |||||  |  ||    | | |         || |    | ||    |   |  | ||   | |        
ATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAGgttcgcttccaatctctttcattcttgtgt-----ttcctcggcggtgcgttttct-cggaccctgtgtatgtagtgtggtagtgtagtattcgaggagaggccac

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtac--ttctgtgg-cctataactt-cttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt---
|||| || |||||||| || || || ||||||||||| |||||||| |||||||||||||| ||||| ||||| || |||||||| ||||||||| |  |  |||   |||   |||| |  ||  |   ||| || ||||         | | ||| |       | | |   | | |    ||||||  |   ||   
ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtcttgttctccttcgacttgcgagtcgggtgatttctcagaaagtcag---aaactagcgcga----ccggactatgctagtcattttttatgctcttgct

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgta----cttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt---
|||| ||||||||||| || || || |||||||| || || ||||| |||||||||||||| || |||||||| || |||||||| || ||||||     |||||      |  |  | |  ||  |   ||| || |  ||    |  ||| |       ||  ||  |  | | |     |  | | |  | |||   
ATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAGgttggctcttcttctctttcgagttgcgagtccggtgatttctgaagaggga-acgtatct------ggtgctcaaaggggtacggtgctcatgtgcacattttaaa

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtg-gcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt-
|||| || |||||||| |||||||||||||||||||| |||||||  ||||| ||||||||||||||||||||||||||||||||||| ||||||| |||  ||    ||| | ||            ||  || | | |||  | |  | |      || ||  |||  || |    ||    |  |   | | 
ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccctgcatttatgaattgggaaaatgtctttttttgggaatctagtgttcaattagattgtgtt--gaaaactactttgttcaaatcagtgttcta

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctga-----atgcttcaaaattttttttcggaattt-
|||| || |||||||| |||||||||||||||||||| |||||||  |||||||| |||||||||||||||||||||||||||||||| ||||||| |||      |||| | | ||| |        | |||   |||   |   |    | |||   || ||       |||  |    |  |||| ||    ||| 
ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttccaacaactattattactttt------gcttcttgttagttgcaagaagcaaaaagataattccttgcatttatgaattgggaaattttatctttttttg

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G17660.2 (Glycine max), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataac-ttcttgtttgaaaattcc---ttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt
|||| ||||||||||| ||||| || |||||||| || |||||||  || ||||| || |||||||| |||||||||||||||||||| |||||| ||  | ||   | ||   || |||||||    | |    |||| | |   | | | |    |   |||||  |  || |    |    | | || |  |  
ATGCTGACATGGAGGACTATGGCTTCGAGTACTCTGATGAGGAGCAAGAAGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAGgttctgttctgctttttactgttgttgtttggcgttgctgaattaggaattgaagccaga---aacttgttttgcggttgatcattatcactgtatcagtgtg-

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataac--ttcttgtttgaaaattccttagaagtcttatctatattag--agaagttttctgaatgcttcaaaattttttttcggaattt
|||| ||||||||||| || || || |||||||| || ||||||   | |||||| || |||||||| |||||||||||||||||||| |||||| ||  | || | ||| |   || |||||   |  |  | | |  |  |||   ||   ||  | |||  |  |   ||  | |  | | |   |  |     
ATGCTGACATGGAGGACTACGGTTTCGAGTACTCCGATGAGGAGGAAGTGGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAGgttctgttctg-cttattattgtttttgttgttatttggcgttgtggaattaggaattggaggcacaagcctgttttgtggctgatcagtatcactgtgtc---

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt
|||| ||||||||||| |||||||| ||||| || || |||||||  ||||| || |||||||| |||||||| || ||||| || |||||||||   | | |  | ||     | |||| |    ||||     || |  |      |||| | |    |  ||| | ||      ||  || |   |    
ATGCTGACATGGAGGACTATGGATTCGAGTATTCTGATGAGGAGCAAGAGGAACAAGATGTTGACATTGAGAACCAGTATTATAACTCTAAAGgttagtttttt-cttacgttctattgtgtttgcattctc--aaacttgtgctgcgattataaa----tcttgactcctagtggtttccttctttaag---

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtactt-ctgtggcctataacttcttgttt-gaaaattccttagaagt-cttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt------------------------------------------------------------------
|||| || ||||| |||||||| |||||||| || || ||||||||||| ||||| |||||||| || |||||||| || |||||| |||||||||| | ||||         ||  ||   | ||| || || | | | | |  ||   | | | |||  |  | ||      || |||||    |  |||||                                                                    
ATGCGGATATGGAAGATTATGGCTTTGAGTATTCTGATGAGGAGCCTGAAGAGCAAGATGTTGACATCGAGAATCAGTACTACAATACTAAAGgtacatgctgtcatgagcccctctttacatagaagatgccctcgtaatgcacatgcttctcatagacctggtgtggcacggtctaaattgcaatgtggaatgcagtgatttctgaatgatgatgccaaaattttgcattccgtgtcttactgtggtgcaacggttatag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgttt---gaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaatttt--ttttcggaattt------------------------------------------------------------
||||||||||||| |||||||| |||||||| || || ||||||||||| ||||| ||||| |||||||||||||| ||||| ||| | |||||||  |   || |    | |||||  ||    ||| ||| |||   |      || ||    |     | |  |  | | |||||  |     | | ||  ||                                                              
ATGCAGACATGGAAGATTATGGGTTTGAGTATTCTGACGAGGAGCCTGAAGAGCAAGATGTCGATATTGAGAATCAGTATTATAATACCAAAGgtatgtgc-tgacacgaagcttctgtttcacagaagatttcttgacaccgccctcgattccggtctgctatgatctacgtttcaatttgaaaatctacgtgatcattgtgagttgtcatgctgaaatcgtctcatgaatgcttatttatgctgcaaatgatgcag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttct-tgtttgaaaattccttagaagtcttatcta--tattagagaagttttctgaatgcttcaaaattttttttcggaattt---------------------------------------------------------------
|||| |||||||| |||||||| || ||||| || || ||||| || |||||||| |||||||||||||||||||||||||| ||| | ||||||| | |  || |    | |  || | |||   || |  |     |  ||| ||   | |||  |  || |  |  ||  |  ||| ||     | ||    |                                                               
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgta-tgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt
| || |||||||| |||||||| ||||||||||| ||||| || || |||||||| ||||| ||||| |||||||| || ||||| ||||||||||     | |   |     ||  |||   | ||  |  | | |     |                                                  
ACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAGgta-----gcgattttc--ttttctgtgaaagaaaacaatggtatcggcag-------------------------------------------------

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 2
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt
| || |||||||| |||||||| ||||||||||| ||||| || || |||||||| ||||| ||||| |||||||| || ||||| ||||||||||       |   | |   ||  |||   | ||  |  | | |     |                                                  
ACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAGgta-------gagattttcttttctgtgaaagaaaacaatggtatcggcag-------------------------------------------------

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|71855965|gb|DT005020.1|DT005020
EST:     GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG                         GTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG
genomic: GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgt ... tttgtcacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG
EST: gi|110724456|gb|EE100301.1|EE100301
EST:     GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG                         GTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG
genomic: GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgt ... tttgtcacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG
EST: gi|161718082|gb|FC068585.1|FC068585
EST:     GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG                         GTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG
genomic: GCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgt ... tttgtcacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttcttgtttgaaaattccttagaagtcttatctatattagagaagttttctgaatgcttcaaaattttttttcggaattt

- - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agagaag