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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCACAGGCTGTAGTTAGTTTTATACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgtttttattgctgtaatttttagtgacttgtaatgattatttcttttcacctttgagttgcagagctagtttctataatttttatatctctag

Basic information

species Vitis vinifera
transcript Vv04s0044g01480.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G26250.1 (Glycine max), 5'ss of exon 3
GCTCACAGGCTGTAGTTAGTTTTATACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttta--ttgctgtaatttttagtgacttgtaatgattat----ttcttttcacctttgagttgcagagctagtttctataatttttatatctctag
| ||||| ||  | || || ||||||||  ||||||||||||| |||||||| || |||||||| |||||||||||    || ||   |  |  |  |||    ||| || ||  | | |    |  ||| ||   ||||||   | ||     || || || |||           
GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAATCATTTTCATTAGTAGCTGAGGAGgtgaaattgtaaactcttacagatttcttggacatgcaaaaactctgctttattttccatgcttgagt-ataaagtccaattttaaaactttag---------

upper sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 3
GCTCACAGGCTGTAGTTAGTTTTATACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttta--ttgctgtaatttttagtgacttgtaatga---ttatttcttttc-acctttgagttgcagagctagtttctataatttttatatctctag
| ||||| ||  | || || ||||||||  ||||||||||||| |||||| | || |||||||| |||||||||||    || ||   |  |  || |||    ||| || || ||   || ||||||||| |   ||||||   | || |   || || || |||           
GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAACCATTTTCATTAGTAGCTGAGGAGgtgaaattgtaaactcttacaaatttcttggacatgcaaagactcttctttcttttccatgcttgagt-ataaagttcaattttaaaactttag---------
















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|351054641|gb|FQ456838.1|FQ456838
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351038015|gb|FQ460757.1|FQ460757
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGGGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351042217|gb|FQ442684.1|FQ442684
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351057082|gb|FQ450789.1|FQ450789
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGGGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351056977|gb|FQ443604.1|FQ443604
EST:     TACTGCAGAGAGAACTTCCCTCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGGGATCTTCCCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351039598|gb|FQ461465.1|FQ461465
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|352794444|gb|FQ481676.1|FQ481676
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351038675|gb|FQ464541.1|FQ464541
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|352793784|gb|FQ481938.1|FQ481938
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|352786467|gb|FQ479076.1|FQ479076
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGGGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
EST: gi|351042941|gb|FQ451235.1|FQ451235
EST:     TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAG                         GATTCGGGGGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT
genomic: TACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgttttt ... atatctctagGATTCGGGAGATCTTCGCAAGGATGGTGCCCAAGAAACACTAGCACGCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCACAGGCTGTAGTTAGTTTTATACTGCAGAGAGAACTTCCATCTGAATCTTTCTCATTAGTGGCTGAGGAGgtttgtttttattgctgtaatttttagtgacttgtaatgattatttcttttcacctttgagttgcagagctagtttctataatttttatatctctag

- - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG