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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag

Basic information

species Vitis vinifera
transcript Vv10s0003g00300.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
|||  | ||||| || |||||||| |||| ||| ||| ||| ||| ||||||||||||||||||||||| |   ||||  | ||||| |||||||| ||||||  ||| |   || ||  |||      |   | ||  ||  || |   | | || | | |         |  |||       | | |||  | | |                                            
ATCTCTCACTGAACTTTCATTCAATTGGACTGGTTTCGTTAATGCCATGATTTCTAATATCTCCTTCACATTACGGAGCGTTTATTCCAAGAAGGCTATGgtttgcttgttacct-ctaatgatctgcatgcatattcactcttccttt-tgatactcccgtttcatttttttactttgttgctgttctttatcacag--------------------------------------------

upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
|||  | |||||||| ||||||||||||| ||||||||| | ||| ||||| || || ||||| ||||| |||||||| || ||||| ||||| ||||||||   ||  | || | |  ||  || | || ||||     |  |  | |      |   ||| |  |                                                                           
ATCCCTTACTGAGCTCTCATTCAACTGGACTGGCTTCATCAATGCCATGATATCAAACATCTCATTCACCTACAGGAGCATTTATTCCAAGAAAGCCATGgt---ctgttgtt-tacgatttgctctcttgtcttaaccatccttctaatcgtttctggcattgcag---------------------------------------------------------------------------

upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G083344_T03 (Zea mays), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgtt---atcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
|||  | ||||| || ||||| || |||| ||||||||||| ||| ||||| || ||||| || ||||| ||| | || |||||||| |||||||| ||||||    ||||       ||  || ||      ||  |  |     |  | |  |   | |  ||  |  |   ||  ||   |     | ||||||| |||  | ||                                     
ATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTCTAAGAAGGCTATGgtttatctctttggcctagcattttacatcaaattgctcctctacattcttagcag--ctcctatttgctgacttactttctta----ttgttttcctttgt--cacag------------------------------------

upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G32190.1 (Glycine max), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttga---ataaaacacacataggtg---gcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
||| ||||||||||| || ||||||||| | |||||||| |||||||||||||| || ||||||||||| ||| | || |||||||||||||| ||||||||||||| || | ||     |     | |    || | |    |  |||   | |||  ||   || ||      | ||   |||  |  ||| |||     | |   | || || |||   |  |                      
ATCTTTGACTGAGCTCTCGTTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATCTCCTTCACATACCGAAGCATCTATTCAAAGAAAGCCATGgttatctcctgtgctagatatacacttctaaatttgtgtgaatttctgatttacaaattacttttatgtcttcctactatactgactattgctctttcatattattattaaataactctttgtgcag---------------------

upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G24360.1 (Glycine max), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctat------tctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
||| ||||| ||||| |||||||||||| | |||||||| |||||||||||||| || || |||||||| ||| | || |||||||||||||| ||||||||||||| ||||      | | | |||     ||| ||    |||||| | |  |  |||  ||   || ||    |   ||| | |  |  || |  |   ||  | |  | |       |  || | ||| | |   ||| |||||
ATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTCAAAGAAAGCCATGgttatctcctatgctagatatacacttctaaatttgtttgaatttctgatttccatgaaattacttttatgtcttcaactcttcatacta--tactgactattgctctttcata------ttattattaaataactc--tttgtgcag

upper sequence: Vv10s0003g00300.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT5G46110.1 (Arabidopsis thaliana), 5'ss of exon 7
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaata-gcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag
 ||| | ||||||||||||||||||||| | || ||||| ||||||||||| || || || || ||||||||| | || ||||  || ||||| ||||||||| |    | |||  ||||  | | |||   ||  |   |  | || |          |  |    | | |  | ||  | ||                                                           
TTCACTAACTGAGCTATCATTCAACTGGCTCGGTTTCATCAGTGCTATGATATCAAACATTTCTTTCACTTACCGAAGCATCTTCTCCAAGAAAGCCATGgttcttcattcttcccctctacattttttacgctactaaatcatgttaaggtttgatttcggaaactgtattgtgtttttgcag-----------------------------------------------------------

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|77583035|gb|DV220554.1|DV220554
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|26265652|gb|CA816715.1|CA816715
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|110388308|gb|EC953043.1|EC953043
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|110376459|gb|EC941524.1|EC941524
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|351031379|gb|FQ445404.1|FQ445404
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|71870783|gb|DT019838.1|DT019838
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|110363008|gb|EC926573.1|EC926573
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|349813488|gb|FQ413722.1|FQ413722
EST:     CACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: CACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|110361951|gb|EC925457.1|EC925457
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|30252871|gb|CB970422.1|CB970422
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|18458226|gb|BM436504.1|BM436504
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|351048322|gb|FQ449414.1|FQ449414
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|30252957|gb|CB970508.1|CB970508
EST:     TTCTAATATCTCCTTCGA-TCACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTCTAATATCTCCTTC-ACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|34542626|gb|CF510858.1|CF510858
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|352794370|gb|FQ481601.1|FQ481601
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|33401641|gb|CF207268.1|CF207268
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|110389432|gb|EC954269.1|EC954269
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
EST: gi|351049192|gb|FQ449914.1|FQ449914
EST:     TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATG                         ACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC
genomic: TTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttct ... gtttttgcagACTGACATGGACAGTACTAATATCTATGCTTATATTTCCATCATTGCTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTCAAAGAAGGCCATGgttatcttctattctgctcttgactgttttttcttttttctggtcttgaataaaacacacataggtggcaatagcttgagaagagctattttcctctgtacctcaaaaattctccttctaatgaatgaatgggtttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG