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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag

Basic information

species Vitis vinifera
transcript Vv11s0016g00900.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgtt-gcattttttggatttgacaaaagacctataattgttgtccttccacag
| ||||| ||||||||||||||||| |||||||| || ||||||||||| || |||||||| || || || ||||| || |||||| || |  | || |||||| | |             |||||| | |  ||  |||     ||||  | ||  | ||  | |   |  | |    ||||| | ||  |  |||   | |  ||     |         
GTGCTGAAATTGGTGGAGCTTTTGGTGGAGAAAAAGCTACTGGTGGTGGACGAGAAGCAGGGAGTGATTCGTGGAAGCAGTACATGAGGAGGGCCACTTGgtaagtagaca---------aattttgattcaagt--atgcaagctataccttgatcaattggtaaaattcctagttccttttgcacttttcccaag--ttgtcgtttgcaac---------

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G130440_T02 (Zea mays), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattat-gttgcattttttggatttgacaaaagacctataatt-gttgtccttccacag
| ||||| ||||||||||| ||||| |||||||| |||||||||||||| || |||||||| || || |||||||| || |||||| || |  | || ||||||    || ||  | |||    ||| || |  || ||  ||   ||  | | | ||| | ||||||||    ||| |   | |   | |    ||    |||||| | |            
GTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAACTGGTGGTGGACGAGAAGCAGGGAGTGATTCCTGGAAGCAGTACATGAGGAGGGCGACTTGgtaag--agtatacacattt----ttgctgtgattgcat--ttgaaatggtacta-tatataatcattattagagcagtgcatag---taagggtagttgcataatttgata-----------

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM5G820733_T01 (Zea mays), 5'ss of exon 5
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgta-tgtttct-tatatttcgagtattttatcattatgttgcat---tttttggatttgacaaaag-acctataattgttgtccttccacag-----------------------------------------------
| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||||| || || |||||||| || |||||| || |  | || ||||||     |  |    |||| | |   |||   || | || | || |||||    | ||||  | || |   | | |    |    || |  | |  ||| || |  ||  | ||   ||    |                                                
GTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGACGAGAAGCAGGGAGTGATTCCTGGAAGCAGTACATGAGGAGGGCGACTTGgtaagagtatacacatttttgctgtgagtgcatttgaaatggtactatatataatcattattagagcagtgcatagtaagggtagcagggtcgggcctaagcacgtgcaacaggtgctattttggaatggatttctaagtagtctactaatgatttgggttttaattttgtcag

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G070514_T02 (Zea mays), 5'ss of exon 6
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgta-tgtttct-tatatttcgagtattttatcattatgttgcat---tttttggatttgacaaaag-acctataattgttgtccttccacag-----------------------------------------------
| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||||| || || |||||||| || |||||| || |  | || ||||||     |  |    |||| | |   |||   || | || | || |||||    | ||||  | || |   | | |    |    ||    | |  ||| || |  ||  | ||   ||    |                                                
GTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGACGAGAAGCAGGGAGTGATTCCTGGAAGCAGTACATGAGGAGGGCGACTTGgtaagagtatacacatttttgctgtgagtgcatttgaaatggtactatatataatcattattagagcagtgcatagtaagggtagcagggccgggcctaagcacgtgcaacaggtgctattttggaatggatttctaagtagtctactaatgatttgggttttaattttgtcag

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM5G828253_T01 (Zea mays), 5'ss of exon 2
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgta-tgtttct-tatatttcgagtattttatcattatgttgcat---tttttggatttgacaaaag-acctataattgttgtccttccacag-----------------------------------------------
| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| || |||||||| || || |||||||| || |||||| || |  | || ||||||     |  |    |||| | |   |||   || | || | || |||||    | ||||  | || |   | | |    |    ||    | |  ||| || |  ||    |||  ||    |                                                
GTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGACGAGAAGCAGGGAGTGATTCCTGGAAGCAGTACATGAGGAGGGCGACTTGgtaagagtatacacatttttgttgtgagtgcatttgaaatggtactatatataatcattattagagcagtgcatagtaagggtagcagggccgggcctaagcacgtgcaacatgtgttattttggaatggatttctaagtagtctactaatgatttgggttttaattttgtcag

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA09G08150.1 (Glycine max), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaa--tttggtttaaccgtt--tgattttgttgc--gggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag
||||||| |||||||| || ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||   || ||| ||    |  |  ||   || |  || | || | |   |  ||   || |||   ||| | || ||   | | |      |   ||      |||||||| ||| |||   |||
GAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGCCGTGAAGCGGGAAGTGACTCATGGAAGCAATACATGCGGCGTTCTACATGgtaagtcttcgttgaatttatgattgttacattccttggttataagctctgttaatggtgaatat---atcttaatattttttctgtgcatgctcgtaatgacattataattgctgttcttg-gcag

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA15G19670.1 (Glycine max), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag
|||||||||||||||| || ||||| ||||||||||| || |||||||| ||||| || ||||| ||||| ||||| ||||||||||||||||| ||||||||| |        |   |||| ||| |    | ||| |  ||  |   ||   |||  | | | || |  ||  | ||  ||   ||| ||                             
GAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGCCGTGAGGCGGGAAGTGACTCGTGGAAGCAATACATGCGGCGTTCTACATGgtaagt--------cttgttgaatttat----gatgtttcatttcttggttataagttctat-taatgacattataattgctgtccttggcag----------------------------

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G54100.2 (Arabidopsis thaliana), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag
||||||||||||||||||||||||| || || || || |||||||||||||||||||| ||||||||||| |||||||| |||||||| || || || ||||||      |||| | | |   | | ||       | |     |||  |||    ||||| ||  ||   ||   ||| |    |||||||                             
GAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGTCGTGAAGCTGGAAGCGACTCATGGAAACAGTACATGCGTCGATCGACTTGgtaaca-atcttaagcttctctctctcttttcataatttccggtttaagtttttgatatttgattctttaattcggtttatct--tttgacag----------------------------

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ31432 (Selaginella moellendorffii), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgt-tgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag
| ||||||||||| || |||||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| || |||||||   |  | ||||||| |    |||    ||    | ||||  ||  |  ||    |  ||  ||||   |  | ||  ||                                                       
GCGCTGAGATTGGCGGTGCTTTTGGCGGTGAGAAGGCTACTGGCGGCGGTCGCGAAGCAGGAAGCGATTCATGGAAGCAGTACATGCACAGAGCGACATGgtgagaaagttctctcgcaaaactttggatgatgtcgtgatctcattccattttttgcttgtttccag------------------------------------------------------

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ38712 (Selaginella moellendorffii), 5'ss of exon 13
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag
| ||||||||||| || |||||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| || |||||||        |||  |  | |||||   |       ||| | ||||               |  ||| ||  || |  | ||    || |||||||||  | |  ||                             
GTGCTGAGATTGGCGGTGCTTTTGGCGGTGAGAAGGCTACTGGCGGCGGTCGCGAAGCAGGAAGCGATTCATGGAAGCAGTACATGC--------ACAGAGCGACTTGgtgagaa-----aattctcttgcaa-------------aactttggatgatctcgtgatctcattccattttttgcttgttccag----------------------------

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|349820814|gb|FQ404199.1|FQ404199
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|33405776|gb|CF211403.1|CF211403
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|351015872|gb|FQ431827.1|FQ431827
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|349816247|gb|FQ403743.1|FQ403743
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGTTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|349819677|gb|FQ402614.1|FQ402614
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|351019460|gb|FQ429595.1|FQ429595
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|349817443|gb|FQ405447.1|FQ405447
EST:     CGTGAAGCAGGAAGCCACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|351027458|gb|FQ444707.1|FQ444707
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
EST: gi|351033661|gb|FQ462191.1|FQ462191
EST:     CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACGTG                         TACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG
genomic: CGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggt ... ccttccacagTACAATCAATTATGGAAATGAGCTACCACTGGCTCAGGGTATCAATTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGTCGTGAAGCAGGAAGCGACTCCTGGAAACAATACATGCGGCGTTCAACATGgtaatttggtttaaccgtttgattttgttgcgggtgtatgtttcttatatttcgagtattttatcattatgttgcattttttggatttgacaaaagacctataattgttgtccttccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC