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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAGTGTTCATGGCCACTGGAAGCATCATGATGTTAAGGTTAAGGATTCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttgaattttcttgaattgtatggctgtttgattggagaagaagtgggagatttgagtttgggattcaatgtgctactttttttggttgattttcag

Basic information

species Vitis vinifera
transcript Vv01s0010g02460.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 5'ss of exon 4
ATGACAGTGTTCATGGCCACTGGAAGCATCATGATGTTAAGGTTAAGGATTCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttgaattttcttgaattgtatggctgtttgattggagaagaagtgggagatttgagtttgggattcaatgtgctactttttttggttgattttcag
|||||| ||| || ||||| |||||||||||||| |||||||| ||||| |||||||| |||||||| |||||||||   ||||| || || ||   |||||  | | |   ||| | |    | |   | ||| ||||   |  |  ||  | | |    |         ||||  |  || ||| | || |          
ATGACACTGTGCACGGCCAGTGGAAGCATCATGAGGTTAAGGTGAAGGACTCCAAGACCCTTCTCTTCGGTGAGAAGGAGGTCACCGTGTTCGGCTGCAGgtttgctgtttttttccct---ctctgctgttgtctgatgatatcatgagcagtataccatatc-----gctcaacct--taatttctctgctcag-------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G071630_T02 (Zea mays), 5'ss of exon 3
ATGACAGTGTTCATGGCCACTGGAAGCATCATGATGTTAAGGTTAAGGATTCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttgaattttcttgaattgtatggc-tgtttgattggagaagaagtgggagatttgagtttgggattcaatgtgctactttttttggttgattttcag
|||||| ||| || || || |||||||| ||||| || ||||| ||||| |||||||| ||||||||||||||||||   ||  | || |||||   |||||  | |   | |  | ||  | | | |  | |     |||  |  |      || || |  | |  |  ||  ||||  ||  |||                 
ATGACACTGTGCACGGACAGTGGAAGCACCATGAGGTCAAGGTGAAGGACTCCAAGACCCTTCTCTTTGGTGAGAAGGAGGTTGCTGTGTTTGGCTGCAGgtttgttactattccttttatagtttgtttcatacccaattaaaccatcgtgtggtgact--aatgcgtaat--aatgacctggtttgcag-------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G176307_T01 (Zea mays), 5'ss of exon 4
ATGACAGTGTTCATGGCCACTGGAAGCATCATGATGTTAAGGTTAAGGATTCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttgaa--ttttcttgaattgtatggctgtttgattggagaagaagtgggagatttgagtttgggattcaatgtgctactttttttggttgattttcag
| |||| ||| || || || |||||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||   ||  | || |||||   |||||  | |   |    |||| | | || | |   |     |||  |  |  | | || | |      |   || | ||||  ||  | |||   |           
ACGACACTGTACACGGACAGTGGAAGCACCATGAAGTCAAGGTGAAGGACTCCAAAACCCTTCTCTTTGGTGAGAAGGAGGTTGCTGTGTTTGGCTGCAGgtttgttaccatgcctttcctaatttatttca-tacccaattaaaccaccatttggggctaatgactaatgagt-aatgacct--tgtttgcag-----------

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|33406621|gb|CF212248.1|CF212248
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161710455|gb|FC059346.1|FC059346
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
EST: gi|161706852|gb|FC055537.1|FC055537
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110701389|gb|EE078905.1|EE078905
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161710748|gb|FC060307.1|FC060307
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110697161|gb|EE073909.1|EE073909
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161721814|gb|FC070505.1|FC070505
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAAAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161716699|gb|FC065571.1|FC065571
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161708621|gb|FC058356.1|FC058356
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCAGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110687944|gb|EE065928.1|EE065928
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110373445|gb|EC937683.1|EC937683
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161709828|gb|FC059319.1|FC059319
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
EST: gi|161713863|gb|FC062559.1|FC062559
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110707375|gb|EE083731.1|EE083731
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161708112|gb|FC055727.1|FC055727
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTAT
EST: gi|161718038|gb|FC067580.1|FC067580
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAG--GAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161707334|gb|FC055164.1|FC055164
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATG
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATG
EST: gi|71857565|gb|DT006620.1|DT006620
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161712390|gb|FC061695.1|FC061695
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161715330|gb|FC065818.1|FC065818
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|110688396|gb|EE066900.1|EE066900
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161719339|gb|FC068279.1|FC068279
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161720005|gb|FC067735.1|FC067735
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
EST: gi|161708879|gb|FC060092.1|FC060092
EST:     TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAG                         GAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA
genomic: TCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttg ... tgattttcagGAACCCAGAAGAGATCCCATGGGCTGAGACCGGTGCTGACTATGTTGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAGTGTTCATGGCCACTGGAAGCATCATGATGTTAAGGTTAAGGATTCCAAGACACTTCTCTTTGGTGAGAAGTCTGTCACAGTTTTTGGTGTCAGgtggggtttgaattttcttgaattgtatggctgtttgattggagaagaagtgggagatttgagtttgggattcaatgtgctactttttttggttgattttcag

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