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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag

Basic information

species Vitis vinifera
transcript Vv18s0001g12780.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||||||||| |||||||| || |||||||| ||||| ||||| |||||||||||||| || || || | ||||||||||||| | ||| |||||||| || |||| | | || ||| | | ||||| || | | || | ||||| | || || | | || ||||| |
ACCTGTCATAAATGGCCTTACGGACTACAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTCGAACACATTGGTCGTATTGAAAACACTAAGgta-gatcatttattgc---------accctaaggaacc-accatgtaatcttgctttagt---atattatgactaattttcaacttttattgttatgaag-----------------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || || |||| || ||||||| | ||| |||||||| | || ||| | || ||| |||| || | ||| || | || | | |||| || | | | ||| | ||| | |||
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcataaca--ctgaattaac------tgtgtttggcct----gtgtctaattt-tgagtttctgggttgtaa--ccaatt--gtcttcttcgattgcgttgtag--------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G157210_T01 (Zea mays), 5'ss of exon 6
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || || |||| || ||||||| | ||| |||||||| | || | | | | || ||||||| | ||| || | || | | |||| || | | | ||| | ||| | |||
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACTAAGgtagaatcat--------aacactgaattatctgcgtttgacct----gtgtctaattt-tgagtttctgggttgtaa--ccaatt--gtcttcttcgattgcgttgtag--------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 4
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgac-catttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || || |||| ||| |||||| | || |||||||| || || | ||| | ||| |||| | | | | || || || | | | || | ||| ||
ACCTGTCATAAATGGTCTCACCGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCACGTTGGTCGCATTGAGAACACTAAGgta-gatcatcgt-atcactgaagtaactgcatgtgctctatgcgtctaatttc-----gagatgggttctgaccaactgccttcttcaattgtgtag---------------------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G349547_T01 (Zea mays), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || || |||| || ||||||| | ||| || ||||| | || | | | | || ||||||| | ||| || | || | || |||| || | | | ||| | ||| | |||
ACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGCTTGAGCAGATTGGTCGTATTGAAAACACCAAGgtagaatcat--------aacactgaattatctgcgtttgacct----gtgtctaattt-tgagtttttgggttgtaa--ccaatt--gtcttcttcgattgcgttgtag--------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G03280.1 (Glycine max), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
|| ||||||||||| ||||||||||||| ||||||||||| ||||||||||||||||| || || |||| |||||||||| ||| ||||| || |||||| | ||| || | | || | | | | || | | || | | ||| ||||| | || | || |||| || | ||||| |
GCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGGTTGAGCACATTGGTCGGTTTGAAGGTACAAAGgtcaggttatgttgcttgtcttgaaaagtttgcttcttc--ctaattcttggtggcattttcaagggaatagttg---tcttactgtattctg-cattaca--catgtcag-------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G03360.1 (Glycine max), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
|| ||||||||||| ||||||||||||| ||||||||||| ||||||||||||||||| || || |||| ||||| |||| ||| ||||| || |||||| | ||| || | | |||| | | | || ||| | | || | || | | |||| || || | | ||| | ||
GCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGGTTGAGCACATAGGTCGGTTTGAAGGTACAAAGgtcaggttatgttgtttgtcttgaagattttgcttcttcc-taattcgtggtggcattcgtaagggagtt-gttgtctgact-gttttctgcaatacaaatgtcag------------

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 3
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag
||| || ||||||| ||||| || | || ||||| |||||||| ||||| |||||||||||||| || || ||||||||||| | ||||| || ||||| | | || | || | || | | || || || | | || | | ||| || ||||| || || | | | | ||
ACCAGTTGTCAATGGTCTGACTGATCATAACCATCCTTGCCAAATCATGGCCGATGCCCTCACAATGATAGAGCACATTGGTCAAGTTGAAGGGACAAAGgttagttaaccatttt----------acccgctgcttgctattatctatgttcctcctcat-atgtcgtcaaaaaaagttcta-cctcatttactgcttgaaggaaactgaa------

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|351056870|gb|FQ443497.1|FQ443497
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|110718848|gb|EE096153.1|EE096153
EST:     CTGATGCCCTCACAATAATTGAACACGTTGGTCAGTTGGAAGGAACAAAG                         -TTGTCTATGTTGGGGAAGGGAACAAAATTGGGCATTC
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTC
EST: gi|351041613|gb|FQ455829.1|FQ455829
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|110723485|gb|EE100851.1|EE100851
EST:     CTGATGCCCTCACAATAATTGAACACGTTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|349824294|gb|FQ417705.1|FQ417705
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351030940|gb|FQ438976.1|FQ438976
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351036443|gb|FQ457156.1|FQ457156
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351034924|gb|FQ458281.1|FQ458281
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGG
EST: gi|351035513|gb|FQ463358.1|FQ463358
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351048346|gb|FQ449438.1|FQ449438
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAA                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351034882|gb|FQ458239.1|FQ458239
EST:     TGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAAACTA-G                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCT
genomic: TGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAA-CTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCT
EST: gi|351035222|gb|FQ458579.1|FQ458579
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGAAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
EST: gi|351032125|gb|FQ460382.1|FQ460382
EST:     CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAG                         GTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG
genomic: CTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactat ... gaaaaaccagGTTGTCTATGTTGGGGATGGGAACAACATTGTGCATTCCTGGCTGCTGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAATTGAACACATTGGTCAGTTGGAAGGAACTAAGgtccgactatttttatctgggtcaagactctatgtatttgaccatttagcatctccttgatcagatattcagttgaaattctagtctaatctgatatgatgaccatgtgaaaaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA