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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatccacaaaattcttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag

Basic information

species Arabidopsis thaliana
transcript AT5G64500.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G06880.1 (Glycine max), 5'ss of exon 13
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctc--agctgtatccacaaaattcttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag
||| ||||||||| |||| || ||  | ||||| |||||||||||  |||| ||||||||||||||||| ||||||||||| ||||||||| || | |||||| | ||| |   || ||||| ||  | |     |||| || |  || | ||   |   |||  ||| ||  |  ||| | | | || | |          ||||| ||| | | | |                                   
TGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTGCCTTCCTCACCTCTCGTTGGACTTATCCAGgttagctttttttaagttgtattcattaca-----gatttagtgtcctcaggttcaagggaaa--aagttt--ggcaaatgagctgatgcct----------ttgaggcattattttgt-----------------------------------

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA07G30370.1 (Glycine max), 5'ss of exon 14
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctca-gctgtatccac-aaaattcttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag
||| ||||||||| |||| || ||  | ||||| |||||||||||  |||| ||||||||||||||||||||||||||||| || |||||| || | |||||| | ||| | | | ||||| ||  | |||| || | |   ||   ||||  |||   || |  | | |        ||  ||||  |  |||      |||  ||                                               
TGTTAAACCAAGTTTGAGGCCGCTGTCTATGGCTATGTCTACTGTTGCTATTCATATCTTTGGAGATGTACCTTCCTCACCTCTTGTTGGACTTATGCAGgttagcttttttaagttgtattcattacaatttttaagtggaag---taattacttttccacaacatgat-------gaccagatttatagtctcctcaggttcaagggg--------------------------------------------

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA13G32670.1 (Glycine max), 5'ss of exon 14
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatccacaaaattc-ttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag
||| ||||||||| |||| || ||  | ||||| |||||||||||   ||| ||||||||||| |||||||||||||| || || ||||||||||| |||||  |  ||   |  | |||      |  || || |    | |    | | || |     ||||   |||  |  ||   |  ||| |  |   |    |  ||| |                                              
TGTTAAACCAAGTTTGAGGCCTCTATCTATGGCTATGTCTACTGTTGTTATTCATATCTTTGGCGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAGgtcagcctttatacttttatttgttgagctcattaacatggggaatcagtatcatggc--aatt---cttttgccaa---cagttacttgtagtggcatggctgaaca---------------------------------------------

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA15G06660.1 (Glycine max), 5'ss of exon 14
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatcc-acaaaattcttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag
            | |||| || ||  | ||||| |||||| ||||  |||| ||||| |||| ||||||||||||||| || || ||||||||||| |||||  |  ||   || | |||   ||||  |  || |    | |    ||||||||     ||||   |||  | |||   || ||| |  | | |       ||| |                                              
------------TTTGAGGCCTCTATCTATGGCTATGTCTGCTGTTGCTATTCATATATTTGTAGATGTACCTTCCTCGCCTCTTGTTGGAGTTCTCCAGgtcagcctttatagttttatttgacaagttcattaacatggtgagtcaatgtcttggc--aatt---cttttgctaa---cggttacttgtattggcattgctgaaca---------------------------------------------

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv00s0282g00040.t01 (Vitis vinifera), 5'ss of exon 11
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatccacaaaattcttgattcagagctctaatgtct-taatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag
||| ||||||||| || | || ||  ||||||| |||||||||||  | || || || ||||| ||||| |||||||||||||| ||||| ||||| ||||||||  ||  |  || |  |           |   | |     ||||||| | || |       | | |   |  || |  |  | |  ||||| ||||  |                                                  
TGTGAAACCAAGTTTGCGTCCGCTATCAATGGCTATGTCTACTGTTGCAATTCACATTTTTGGTGATGTTCCTTCCTCACCACTTGTTGGGGTTCTCCAGgtttgcctttcc--ctttccctttctgtcagctagataatcctactaatgtttctagtttcccacatcatttatgtaaagaaaacagt--tctagcttagactc-------------------------------------------------

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|86084242|gb|DR380001.1|DR380001
EST:     TCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAG                         GACTACGTGAACAATTGGAGAGTGACTTCTCTTGTTCTTACATTCGTTCTC
genomic: TCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttc ... actcacgcagGACTACGTGAACAATTGGAGAGTGACTTCTCTTGTTCTTACATTCGTTCTC
EST: gi|164004339|gb|ES134154.1|ES134154
EST:     CCTCACCACTCGTTGGAGTTCTTCAG                         GACTACGTGAACAATTGGAGAGTGACTTCTCTTGTTCTTACATTCGTTCTC
genomic: CCTCACCACTCGTTGGAGTTCTTCAGgtttggtttc ... actcacgcagGACTACGTGAACAATTGGAGAGTGACTTCTCTTGTTCTTACATTCGTTCTC
EST: gi|116470163|gb|EG512755.1|EG512755
EST:     TCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAG                         GACTACGTGAACAATTGGAGAGTGACTTTTCTTGTTCTTACATTCGTTCTC
genomic: TCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttc ... actcacgcagGACTACGTGAACAATTGGAGAGTGACTTCTCTTGTTCTTACATTCGTTCTC
EST: gi|125230862|gb|EL244947.1|EL244947
EST:     CCATATCTTTGGAGATGTACCTTCCTCAACCACTCGTTGGAGTTCTTCAG                         GACTACGTGAAC
genomic: CCATATCTTTGGAGATGTACCTTCCTCA-CCACTCGTTGGAGTTCTTCAGgtttggtttc ... actcacgcagGACTACGTGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAAACCAAGTCTGAGACCACTTGCAATGGCGATGTCTACTGTCTCTATCCATATCTTTGGAGATGTACCTTCCTCACCACTCGTTGGAGTTCTTCAGgtttggtttctcagctgtatccacaaaattcttgattcagagctctaatgtcttaatcaaattaagcttcagttaaacgcgattattcatctagattagtttgagccatcactgtatccaacttcagaatgttttctcatttactcacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG