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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag

Basic information

species Vitis vinifera
transcript Vv13s0019g04680.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 5'ss of exon 4
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtat-----cattgg-----ccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaa---taactcaacttatagtcttcttgagtctattgaa--atggatctagagctctctctcttccatgaaaacccatttg--agaaaattacagaggataact--tcattcctcag
|||||||| || || ||||| |||||||||||| | || ||| | ||||| || ||||| ||||||||||||||||| ||||||||||| |||||||        ||| |        |   | | |||| ||   |      |   | |  ||   | | || |||    |    || ||| |  |   | |  ||||  |  |   | ||| || |    |  |      |||     | ||| |  |  |||  |   | || ||||  | | |  ||||
GTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAGgtgcataaatattagaagctttgattaactattttcccaagtgcatccttgcattaactctgtactatggaatttctgtaccatcttttgcttcacatatgtcttcttcacccttgatttacattgtttgcaagcatatgtgttgctattcgttaccaaagaagtcacgagaactggttaattttcag

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 5
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgta--tcattggccaacccattttttttcctgttcacctatctg----acttt-ctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccat--ttgag--aaaattacagaggat---aacttcatt--cctcag
|| ||||| || || || || || ||||||||| | || ||| | ||||| || | ||| ||||||||||| ||||| |||||||| |||||||||||  |   ||   |   || |  || |  ||   |||||  ||    ||||| |   |   |     |  |  ||   |  || ||||      | |  |  |       | |    | |       |||| |      |   |||   || | |   ||| ||    |  |  |     ||||
GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAGgtaatttggtgctgagatcagtacttattttggatacctaattgggatactttgccgcacgtacccacaggatttctgatagtattctttgcacatttgatccatctttctttgcaagcacaacagcacatgcatgtttttgcctgaatcaagagtcatgagaattgagagcttgtcaatttcag

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 4
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag
|| ||||| |||||||| || |||||||||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||  |  |          || | ||||| | | |   ||   |  |  |  |   |  |    |   |||||  | | |  | ||      | | ||||   | |     | ||||| || ||                                              
GTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgtgactctcat-------ttatctttccagattaatcat--aatctattgtacaaaccattcttttttcaacaaaaaatgatttttga---aataaaatttgtttgctaat-tctctatttcag---------------------------------------------

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 4
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag
|| ||||| |||||||| || ||||| |||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||       | |   |  || | ||||| | | |   ||   || |  |  |   |  |    ||  |||||    | | || ||      | ||||||   | |     | | ||| || ||                                              
GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAGgt-------gactgtcatttatctttccagattatgcat--aacctattgtacaaaccattcttatttcaacaacaaatgttttttga---aatgaaatttgtttgctaat-tatctgtttcag---------------------------------------------

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 4
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttc-ttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag
|| ||||| ||||| || |||||||| ||||| || || |||||||| ||||| ||||| ||||||||||||||||| || || || || ||||||||| |     |    |||     ||  | ||  | ||| | | |   ||||  |  |  |||      |   | ||  || | || | | ||||   |                                                                       
GTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAGgtatta---aacccttcatgcagatttgtatt-gcttattttattagataaacgctttgcaaacttactaggatttaacctgcattcactttatttttag----------------------------------------------------------------------

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|294963923|gb|GW836798.1|GW836798
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351049141|gb|FQ449863.1|FQ449863
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351031329|gb|FQ445354.1|FQ445354
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110378503|gb|EC943640.1|EC943640
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110386522|gb|EC951122.1|EC951122
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110707796|gb|EE084605.1|EE084605
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351029650|gb|FQ427490.1|FQ427490
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351031354|gb|FQ445379.1|FQ445379
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351036602|gb|FQ457315.1|FQ457315
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110390981|gb|EC955931.1|EC955931
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351033397|gb|FQ462048.1|FQ462048
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|30302011|gb|CB978805.1|CB978805
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|349830843|gb|FQ418151.1|FQ418151
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110428129|gb|EC994591.1|EC994591
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|351016862|gb|FQ424289.1|FQ424289
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACCATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
EST: gi|110691925|gb|EE070587.1|EE070587
EST:     GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG                         GTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT
genomic: GATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattgg ... cattcctcagGTATGCTGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAGgtatcattggccaacccattttttttcctgttcacctatctgactttctaaattcaatagaaataactcaacttatagtcttcttgagtctattgaaatggatctagagctctctctcttccatgaaaacccatttgagaaaattacagaggataacttcattcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA