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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc...

Basic information

species Vitis vinifera
transcript Vv12s0028g01810.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 6
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagt--gttgaagaccatgtgtgctccttcttcttt-tttgatgcgtgttc--cttcttcttatccctgtctctttctctctctctctttattttttgggctc
|||||||||||||| ||||| || ||||| ||||| |||||||||||||||||||||||| ||   ||     || |  | |    ||||   |  |||||||  || |    || ||||  |    | ||  |  |     |  |   ||   | |     
GTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTGgtatgttgatttccacccttaagagtaatttctcagtggtttgatgtatgctgaaattattctagtggtaggctagtcataatgttgacagcataagtgg-----

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 6
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc---------
||||||||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||||||  |||||       | | |  | | ||     | |  |  |   | | ||  | |||| |   | | |     | |   | |  |   |||   |           
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgta--tgttg-------tttttctttcctcgaggatctgtagtcacatccttttgttttatgctcttttttaaaaatattgttatcaaaggtttaatcatgtgcagtta

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G045330_T01 (Zea mays), 5'ss of exon 5
-------------------------------------------GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc---------
                                           ||||||||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||||||  |||||       | | |  | | ||     | |  |  |   | | ||  | |||| |   | | |     | |   | |  |   |||   |           
AATTAGTTCTGAATTGGTCTCGTCGTCTCTCTTTGATGTACAGGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTGgta--tgttg-------tttttctttcctcgaggatctgtagtcacatccttttgttttatgctcttttttaaaaatattgttatcaaaggtttaatcatgtgcagtta

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 6
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtg---ttgaagaccatgtgtgctccttcttctttt---ttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc
||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| || |||||| ||    ||     || || |   |  |  |    |    ||| ||  || |   |||| | |    |   | |      ||   | ||  ||  ||      
GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtttttctttccttgaggatttgtagtcacatccagttgttgtatgctttctcttttgaaatattcttatcaaaggcttgtttttctttcctt------

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G36570.1 (Glycine max), 5'ss of exon 5
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc--
|||||||| ||||| || || || ||||| ||||||||||| |||||||| ||||||||| || | | |  |    |||||   |   |  ||| | |   || | |   | | ||| |  ||    |       |       |||  |     | |  
GTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTGgtatgt-tggtattcttcctgtgcatttcactactttat-acatgtatgctaccatgttaacagtggacgtggaatattaatatcatatgctacctaccccg

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc----------------------------------------------------------------------------------------
|||||||| ||||||||||||  |||||| |||||||||||||||||||| || |||||||| | |  ||||  |   |   ||   || || ||||     |   |  |  |  | ||  ||  |       |      ||  | ||    |  |                                                                                         
GTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTGgtaagaggtttagacttttatttaccccatttgttgtttgtcttttccactgtgcttgtgtctttgcatgcagtagttaaaaactccaattaagtgaatattatgcaagtaatttacataagtatggatgcagtttcagatatttctctgttagcctgatatttgcaacatttggctttttatattag

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattt---tttgggctc----------------------------------------------------------------------
||||||||  | ||||||||||||||||| |||||||||||||||||||| ||  ||||||| ||   |     |   |    |  ||| ||| |   |    |       |   ||||   |  |||   || ||        || |   | || | |                                                                       
GTTGATCCCTTGACCCATCAGGTTAAGCTGTGTGATTTTGGAAGTGCAAAAGTATTGgtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactgagctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattag

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|37185091|gb|CF604444.1|CF604444
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|110711443|gb|EE087924.1|EE087924
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCG
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|110725002|gb|EE101323.1|EE101323
EST:     CTCTCACCCATCAAGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|349830587|gb|FQ416885.1|FQ416885
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|351023941|gb|FQ423364.1|FQ423364
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|27582878|gb|CB005573.1|CB005573
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|33402557|gb|CF208184.1|CF208184
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|351020144|gb|FQ445751.1|FQ445751
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|110719282|gb|EE097083.1|EE097083
EST:     CTCTCACCCATCAAGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGATCTG                         GTCAAGGGTGAA-CAAACATATCATACATTTGTTCTCGCTACT
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACT
EST: gi|351025140|gb|FQ433557.1|FQ433557
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|351036312|gb|FQ458687.1|FQ458687
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|71856792|gb|DT005847.1|DT005847
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC
EST: gi|110718800|gb|EE096049.1|EE096049
EST:     CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG                         GTCAAGGGTGAAGCAA-CATATCATACATTTGTTCTCGCTACTACCGGGCC
genomic: CTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttg ... cgctcatcagGTCAAGGGTGAAGCAAACATATCATACATTTGTTCTCGCTACTACCGGGCC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTGgtaagtgttgaagaccatgtgtgctccttcttcttttttgatgcgtgttccttcttcttatccctgtctctttctctctctctctttattttttgggctc

- - - - - - - - - - - - - - - - - - - TGGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc