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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatttatgcatatacaattag

Basic information

species Vitis vinifera
transcript Vv06s0004g07790.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatttatgcatatacaattag-------
 |||||||| ||| ||||||| ||||| || || || || |||||||| || || |||||||| || || || |||||||||||||||||||||||| |||||     ||| | |   || ||     || || | | |  || |    |  ||    | | | |  ||   ||  |    | ||||  |       
GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgataccattacaggtcaaa----gcattccttaaattgtacctttcg-ctagcttgtgcattaatggctt-cgtcggtgcaatgcggtttcag

upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g07270.1 (Oryza sativa), 5'ss of exon 1
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaa--agccccagttcccatctaatcttacagtcttcata-acgttctacccttctgatgttttcttctataa-tttatgcatatacaattag--------
 |||||||| ||||| || || ||||| || |  || || |||||||| ||  | || ||||| || || || |||||||||||||||||||||||| |||| |  ||     |  |     ||| |||| | |   ||||  | | |  || |  |||  |      | | |   ||||    ||  |||| |        
GGAGTGCCCCTTCTCGCCGTACTTCTCGCCGCTGGAGCCGCACAAGTTCGCCTCCGTGCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtgagtagtgatcgagctgggttaagctta-attaagcatatgcatccatccatggtgacctagctagcaagaggcttatattaat-taattggttgaactc

upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G868471_T01 (Zea mays), 5'ss of exon 1
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatttatgcatatacaattag-------------
 |||||||| ||||| ||||| ||||| || |  || || |||||||| || || |||||||  || || || |||||||||||||||||||||||| ||||||| ||       ||||    | |  | |||  |   ||     | | |  ||  |||   || || ||||||     |     ||               
GGAGTGCCCCTTCTCGCCCTACTTCTCGCCGCTGGAGCCGCACAAGTTCGCCGCCGTCCACAGGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtaaatccatcaaatccatgcgttttggctgtcacctatac---tcaacttcttggggttaaattataaaatttagtaccaccttttttattttgaggagatt

upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatt-tatgcatatacaattag-----
 || ||||| ||| |||| || ||||| || ||||| || ||||| || || || |||||||| || || || || ||||||||||||||||||||| |||||||||| ||  |   |   ||  |     | |||       ||||   ||   |  |||   | || | || ||  | | | | |||       
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaaagcctcaacttgaagaaaaaatcgtgcttttc----tagtctatagttaaaagatttcagtgtagacttgtaaacgtgt-cgattgtcacag

upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ35900 (Selaginella moellendorffii), 5'ss of exon 1
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagtt-cccatctaatcttacagtcttcata-acgttctacccttctgatgttttctt---ctataatttatgcatatacaattag-----
|||||| || ||  | || || ||||| || || || ||||| |||||||| || |||||||||||||| || ||||||||||||||||||||||||  ||||      || |   || |||  |||| | ||    ||    |  | ||  |||   ||| ||  |      || | | | |   | |     |     
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaatcatccctcttctcttcccgtggcaatccgagcaccactattccattgtctttctaagtggtactcttttctctttcggagtgtgctt

upper sequence: Vv06s0004g07790.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ09483 (Selaginella moellendorffii), 5'ss of exon 1
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagt------tcccatctaatcttacagtcttcata-acgttctacccttctgatgttttcttctataa---tttatgcatatacaattag
|||||| || ||  | || || ||||| || || || ||||| |||||||| || |||||||||||||| || ||||||||||||||||||||||||  ||||      || |      |||| ||   |||| | ||   | |    |  | ||  |||   ||| ||  |   |     | | | |   | |     |
AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaatcatctctcccctcctctcttcccgtggccctccgagcaccactattccattgtctttctaagtggcactcttttctctttcggagtg

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|110379260|gb|EC944443.1|EC944443
EST:     ATGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
EST: gi|110395266|gb|EC960924.1|EC960924
EST:     CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
EST: gi|110373981|gb|EC938425.1|EC938425
EST:     CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
EST: gi|110359079|gb|EC919967.1|EC919967
EST:     CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
EST: gi|110359881|gb|EC922157.1|EC922157
EST:     CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: CTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
EST: gi|110385435|gb|EC949960.1|EC949960
EST:     TTTTGGTGCCAGCAACGTCTCCAAGATGCTCATG                         GATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA
genomic: TTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagcccc ... atacaattagGATGTTGCAGAGAACCAAAGAGCAGATGCCGTGAACAGCCTGGTTTTTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTGCCCTTTCTCCCCCTATTTCTCCCCCCATGAACCTCACAAGTTTGCTGCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCCAAGATGCTCATGgtaaagccccagttcccatctaatcttacagtcttcataacgttctacccttctgatgttttcttctataatttatgcatatacaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG