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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttctgttcatccttatagtctaggaacccatagttaggtcagaaatgcttttccttttcatctgaactaggcatgccatttaaatactatctga...

Basic information

species Vitis vinifera
transcript Vv12s0055g00390.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G05430.1 (Glycine max), 5'ss of exon 5
ACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagc---ttctgttcatccttatagtctaggaacccatagttaggtcagaaatgcttttccttttcatctgaactaggcatgccat-ttaaatactatctga
|| ||| |||||||||| || || || |||||||||||||| ||||||||| ||||||| ||| | ||||||||||||| |||||||||||  ||||| ||||||    || |    |||||   || ||  |||     |    | |     ||| |     |            |   || | ||  ||  |||   |    
ACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCATATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagtaattttttcctatcctagaagccttagaaattggatcatgattcttgatggtgaatttgggtcctaagcttgatcacgacaaattgcatatcgt----

upper sequence: Vv12s0055g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G19620.1 (Glycine max), 5'ss of exon 4
ACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagct--tctgttcatccttatagtctaggaacccatagttaggtcagaaatgcttttccttttcatctgaac-taggcatgccatttaaatactatctga
|| ||| |||||||||| || || || ||||| |||||||| ||||||||| ||||||| ||| | ||||||||||||| |||||||||||  ||||| |||||| |  | |    |||||   || ||  |||     |  | | | | |     || | |||     |  ||  |   ||||    || |     |  |  
ACAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTACGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAATGAGGATGATGCTACAAATTgtaagttattttccctatcctcgaagccttagaagttggatattgattacac---tttgtacttgaagcccaaagatgatcatgattcttgatggtgaatttg

upper sequence: Vv12s0055g00390.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G23150.1 (Glycine max), 5'ss of exon 3
ACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagc--ttctgttcatccttatagtctaggaacccatagttaggtcagaaatgcttttccttttcatctgaactaggcatgccatttaaatactatctga
 | ||| |||||||||| || || || ||||| |||||||  ||||||||| ||||||| ||| | |||||||||||||  ||||||||||  ||||| ||||||   || |    |||||   || ||  |||     |  | | | | |  |  | | | |      |  |  |   ||||    || |     |  |  
GCAAAGGAGATGTTTCAGCTGCTTCTCTCTGCTTATTCTATGATAAGCATTAAAGACACTGCTTTATTTCTGGGAATGAACGAGGATGATGCTACAAATTgtaagtaattttccctatcctagaagccttagaagttggatgttgattaca--ttttgtacttgaagcccaaagatgatcatgattcttgatggtgaatttg

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|83276839|gb|DV940847.1|DV940847
EST:     AATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: AATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|34415352|gb|CF414106.1|CF414106
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|110422359|gb|EC988680.1|EC988680
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|110726796|gb|EE102901.1|EE102901
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGAGTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|87585298|gb|DY474073.1|DY474073
EST:     AATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: AATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|110413954|gb|EC979773.1|EC979773
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|32272342|gb|CD721501.1|CD721501
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|32247432|gb|CD713251.1|CD713251
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|30326219|gb|CD009481.1|CD009481
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|71883301|gb|DT032356.1|DT032356
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|110408688|gb|EC974328.1|EC974328
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG
EST: gi|110370922|gb|EC934544.1|EC934544
EST:     TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACT                         ATGTGGTAGAGCAAGGTTGGACTGTGGATTCGGCCTCTCGAATGCTAACTG
genomic: TCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttct ... tcatttgcagATGTGGTAGAGCAAGGTTGGACAGTGGATTCGGCCTCTCGAATGCTGACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGAAGATGTTTCAACTACTGCTATCTGCATATTCTACAATAAGCATTCAAGACACAGCTCTTTTTCTGGGAATGAGTGAGGATGATGTGACAAACTgtaagcttctgttcatccttatagtctaggaacccatagttaggtcagaaatgcttttccttttcatctgaactaggcatgccatttaaatactatctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcagaaa