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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt...

Basic information

species Vitis vinifera
transcript Vv07s0005g00230.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatg----tctgaaatcttcctcacatgtttaagctaaatctatgaccttacagt-gcat-tcttgttacgttctttgcttagttgtcttttggtcctattttgt
||||| |||| ||||||||| ||||| || || |||||||||||||| || || || |||||||| |||||||||||||||||    | | | || ||   | | ||||||   |     | ||   |    || | || | | |  | ||   ||    |  ||  |  |   ||| |     
GATGGTGATAAGTTTTGGAGGATGCCAGAATGTTACATCCGTGGGAACACCATCAAGTATCTTCGGGTTCCTGATGAGgtatggatttttaacatgttaaac-cttgtttactatgtgcttgtggtttgctggttgtatgtttagacatgtatgttctccatctgcataatcagccttt-----

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G095114_T01 (Zea mays), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaa-tctatgacc-ttacagtgcattcttgttacg-ttctttgcttagttgtcttttggtcctattttgt
||||| || | ||||||||| ||||| ||||| ||||| |||||||| || ||||| ||||||||||||||||||||||||||    |  ||||  | |        ||||| | |||||  |  ||    |   || ||  | || ||||  ||||     |  |||  | |  | |  |
GATGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGTGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatg---aatttcttggttaatgagggtagctacactctatttcagttttgcttggttgtttatgcgcttctaggcttctactttatttttttccttgtcat

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G038606_T03 (Zea mays), 5'ss of exon 3
----------------------GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctca-catgtttaagctaaatctatgacc-ttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt-
                      || || || | ||||||||| ||||| ||||| ||||| || ||||| || ||||| ||||||||||||||||||||||||||   ||  ||||  | |    |  ||  | |  |||||  |  ||    |   || ||  |  | |  |  || | || |   |||    |||    | 
TTTATGATGGCTCGAATTGCAGGACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatg---gatttcttggttaatgagcctagccaatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttccttgtcattatgacatg

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G038606_T02 (Zea mays), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttc-ctcacatgtttaagctaaatctatgacc-ttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt-
|| || || | ||||||||| ||||| ||||| ||||| || ||||| || ||||| ||||||||||||||||||||||||||   ||  ||||   | |   |  ||  | |  |||||  |  ||    |   || ||  |  | |  |  || | || |   |||    |||    | 
GACGGTGACAAGTTTTGGAGGATGCCAGAGTGTTACATTCGCGGGAACACCATTAAGTATCTTCGAGTTCCTGATGAGgtatg---gatttcttggttaatgagcctagccaatctctatttcagttttgcttggttatttatgtgcttctccctgatttcttccttgtcattatgacatg

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G17430.2 (Glycine max), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgt---------ctgaaatcttcctcacatgtt-------taagctaaatctatgaccttacagtgcattcttgttacgttctttgct-----tagttgtcttttggtcctattttgt---------------
||||||||||| |||||| | ||||||||||||||||| ||||| ||||| ||||| || ||||| |||||||||||||| |||              || ||  |    || |       | |   |  |  |  || |   || | ||        |  ||  || |      | || ||   || |   | |||                 
GATGGAGATAGATTTTGGCGTATGCCTGAGTGCTACATTCGTGGCAATACCATTAAGTACCTTCGGGTTCCTGATGAGgtgtgtgctgctgcttcagtatttttgttttttgctctttcagtgaataaggttcagaacttcttagggaatgtcgtaagctctcggtgatgcatgcatttatccactgatttaaatttacttcctgttcatttag

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA19G39780.1 (Glycine max), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcatt--cttgtta-cgttctttgcttagttgtcttttggtcctattttgt
|| |||||||| |||||||| |||||||| ||||| || || || |||||||| || || |||||||||||||||||||| ||| |    | | |    |   |   |  | | | | | |  |   | |  |    ||||| |  |   |  |   |   |    |||   |  |     
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTATATACGAGGCAATACAATCAAGTACCTTCGAGTTCCTGATGAGgtgtgtattgtgtgtgcagtgctaatgacattttatttttttatttgttaatttaaaaacttgtaaatgggttgagaagaagggaaccttgccacggtag---

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G37170.2 (Glycine max), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgacct-tacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt
|| |||||||| |||||||| |||||||| |||||||| || || |||||||| || || |||||||| ||||||||||| ||| |    | |      |  ||   |  |   | | | |  | |  | |  |    || ||  ||  |||   ||           | | |   |  
GACGGAGATAGATTTTGGAGGATGCCTGAATGCTACATACGAGGCAATACAATCAAGTACCTTCGAGTACCTGATGAGgtgtgtattgtgtgtggtgtgctggtgacattttctttttttatttgttaattttaaaactggtaaatttgttgagaagaaagggagccttgccacagta-

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G02380.1 (Glycine max), 5'ss of exon 4
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgt----ctgaaatct---tcctcacatgttt--------------aagctaaatctatgaccttacagtgcattcttgttacgttctttg-------cttagttgtcttttggtcctattttgt---------------
||||||||||| |||||| | ||||| ||||||||||| || || ||||| || || || ||||| |||||||||||||| |||    |||     |   || |   ||||||               |   |  |  |  || |   |||| ||   || || | |||| |        | | || ||   || ||    |||                 
GATGGAGATAGATTTTGGCGTATGCCCGAGTGCTACATTCGCGGCAATACCATAAAGTACCTTCGGGTTCCTGATGAGgtgtgtgctgctggtgcttcagtcgttttatgtttttttctctttcagtgaataaggttcagaacttcttagtgaatg--tggtaagctcttagtgatgcattcatttatccactgatctagctttacttcctgttgatttag

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt-
|| |||||||| |||||||| ||||| || || || |||||||| || ||||| || || ||||||||||| |||||||||  | |    |  |       ||| ||       |   ||| ||     |   ||  |    |  ||| ||    | ||    || | |  ||    | 
GACGGAGATAGATTTTGGAGGATGCCGGAATGTTATATCCGTGGTAACACAATCAAGTACCTTCGAGTTCCGGATGAGgta-atttttttttgtgtgtgtgtgtatatatctcttgcttgatctagttttttctttgttcccctctctctggaatgatgatgcttagccaaatcagata

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 5'ss of exon 3
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgt--atgtctgaaatcttcctcacatgtttaagctaaatctatgaccttaca----gtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt-----------------------------------------------
||||| ||  |||| ||||| |||||||| |||||||| || || ||||| || |||||| | || ||||||||||||||   | | |   ||    ||   |  |    | |  |    ||  || |||    ||  | | || ||       || |  |   ||    ||  |||  |||||                                               
GATGGTGACCGGTTCTGGAGGATGCCTGAATGCTACATTCGAGGAAATACTATAAAATATTTGCGGGTTCCTGATGAGgttagtatttacgattcaacttctagctagcggttttaatcctgttctgacaatcagtatactgttattcatactcttacgaaagcgtgcaatgtgcctgatttgttaatagtttctgaaagccatcatcattgctattgtttcctccttcag

upper sequence: Vv07s0005g00230.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ10085 (Selaginella moellendorffii), 5'ss of exon 3
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt
||||||||  |||||||||||||||| |||||||||||| | || || || || || |||||||| ||||| || |||||  |         ||||   |  |||   ||  |   | |    |   || |     |  | ||   ||| | ||                        
GATGGAGACCGGTTTTGGAGAATGCCCGAGTGCTACATCAGGGGCAACACCATCAAGTATCTTCGTGTTCCAGACGAGgtgagc-----gatttccattcgcgttactgccgagcttgt---ttgtgagggagagatcctcactcacttcgtttgaaccag-----------------

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|349828814|gb|FQ419147.1|FQ419147
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|349819985|gb|FQ404707.1|FQ404707
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|349819983|gb|FQ404705.1|FQ404705
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|110372194|gb|EC936345.1|EC936345
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|110383606|gb|EC947989.1|EC947989
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|349827595|gb|FQ422463.1|FQ422463
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351029470|gb|FQ436864.1|FQ436864
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|110692708|gb|EE068197.1|EE068197
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351012236|gb|FQ426958.1|FQ426958
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351044635|gb|FQ443166.1|FQ443166
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351025082|gb|FQ433499.1|FQ433499
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|349828184|gb|FQ415512.1|FQ415512
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351056955|gb|FQ443582.1|FQ443582
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|110374587|gb|EC939452.1|EC939452
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|351038850|gb|FQ448493.1|FQ448493
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|110372487|gb|EC936658.1|EC936658
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|352790730|gb|FQ478278.1|FQ478278
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
EST: gi|349828185|gb|FQ415513.1|FQ415513
EST:     AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAG                         GTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG
genomic: AGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctga ... tgcatttcagGTAATTGATAAAGTTCAAGAAGAAACCAAGAACCGAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAGATAGGTTTTGGAGAATGCCTGAGTGCTACATCCGTGGGAATACAATTAAATATCTTCGAGTTCCTGATGAGgtatgtctgaaatcttcctcacatgtttaagctaaatctatgaccttacagtgcattcttgttacgttctttgcttagttgtcttttggtcctattttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc