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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggtt------ttagtttaagttgaaacatttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag---
||||| || |||||||||||||||||||| ||||||||||||||||||||| | ||||| |||||||||||||||||||| | |||||| ||  |  ||  |      ||  ||||   |  |  |  ||  ||       |  |    |  | ||||| |     || |  ||       
CCTGAGGACTGGGATGATGAGGAAGATGGAGAATGGACAGCTCCAACCATTCCAAACCCTGAGTACAAGGGACCATGGAACCAAAAGgtatg-agtgtgactgaatagttcatttactctagacaagctaggttcagcatcacgattactcac-taattgcatgaaattttgtgtgtttag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttt-------tagtttaagttgaaacattta-attttgctggtaaaagagttgtcataattcctctctatctcttggcag
||||| || ||||||||||||||||||||||| ||||| || ||||||||| | ||||| |||||||||||||||||||||| |||||| ||       ||||        || |  | |||||||| ||  || || |||||        || |||||      |   | |    |   
CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggttt-----ctgacataaacatgtttctttttccag---

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagttta--agttga-aacatttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag
||||| || ||||| ||||||||||||||||||||||| || || |||||| ||||||| || ||||||||||||||||| | |||||| ||     |  |||||   ||  |  ||| | || || || || ||| ||       || ||  ||     |  |  |    |   
CCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAGgtatggcagttccttttaacctataaactgacagcaattcatatt-ctgatat-----ctgacagcatgttgtttcacttgccag---

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaac--atttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag
||||| || |||||||| |||||||||||||||||||| || || |||||| ||||||| || ||||| ||||||||||| | ||||||   |||||     ||    |   |  ||||  |  | | ||   |  |   | |  || ||  ||   || ||  |         
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgt--atggcagttccttgaactgtatacaaactgacatcaattca-tattctgatatctgacagcatgtttcacttgccag------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca--tggtttt---agttt-----------aagttgaaacatttaattttgctggtaaaagagttg--tcataa--ttcctctctatctcttggcag
|||||||||||||||||||||||||||||||| |||||| | || |||||||||||||| || |||||||| ||||||||| ||||||||||||| |  | |||||   | |||           ||  ||| | |||  ||| || | | ||   | |||  | ||||  || |   |||  | || ||||
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatattccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 7
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagtt-gaaacatttaattt------tgctggtaaaagagttgtcataattcctctctatctcttggcag---------------
|||||||||||||||||||||||||||||||| |||||| | || |||||||||||||| ||||||||||| ||||||||| || |||||||||| |   ||||| | ||| || | || |||| |  |      |  |     | |  | || || | |   || | |  ||| |||                
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAGgtttgtggaa-atttttattgtaaatttgtaatatttgaaatacgacatattccattatgtttggtaatgaatttgctttctaactttgcatgctacatatttgcag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaa---gagttgtcataattcctctctatctcttggcag
||||| || ||||||||||| ||||||||||| ||||| || || |||||| |||||||||||||||| ||   ||||||||| |||||||||    |||||||  | |       |  ||||||  | |    |  |     | |  ||  |       | |||   |  | ||
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgt----tggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaagagtt-----gtcataattcctctctatctcttggcag
||||| || ||||||||||| ||||||||||| ||||| || ||||| ||  ||||||| ||||||| |||   ||||||||| |||||||||       || || |  ||    ||  || ||  | | ||||| || |  ||      ||  ||  |      || | || | ||
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCAACAATCCCCAACCCTGAGTACATGGGTGAATGGAAGCCTAAGgtttgtca---atttctattccaaa---aagtatcta--tatcctggtcaacgtttttcttcctctcaaggctgtcaaatatttttgtag

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|33401772|gb|CF207399.1|CF207399
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110372400|gb|EC936562.1|EC936562
EST:     CAGCTCCAACCATTGCCAACCCCCAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAA
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAA
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|349816036|gb|FQ413550.1|FQ413550
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|351027478|gb|FQ444727.1|FQ444727
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110700083|gb|EE077719.1|EE077719
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|349808465|gb|FQ405609.1|FQ405609
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGGAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|33401998|gb|CF207625.1|CF207625
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAACGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110687446|gb|EE064865.1|EE064865
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110357396|gb|EC920905.1|EC920905
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|351043138|gb|FQ451311.1|FQ451311
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|351022735|gb|FQ428644.1|FQ428644
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|33402080|gb|CF207707.1|CF207707
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAACGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|77578221|gb|DV217893.1|DV217893
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|161716555|gb|FC065240.1|FC065240
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|71870544|gb|DT019599.1|DT019599
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAG                         AAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC
genomic: CAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggca ... ctcttggcagAAAATTAAGAATCCCAACTACAAGGGAAAATGGAAGGCACCAATGATTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaagagttgtcataattcctctctatctcttggcag

- - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG