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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaactaaactatatgctgctctaaaccgaatgatatatctggtgcag

Basic information

species Arabidopsis thaliana
transcript AT2G44120.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 5
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc-----tgattctctctctttcaataggattatgtaaactaa--actatatgctgctctaaaccgaatgatatatctggtgcag---------
|||||||||||||| || || ||||| |||||||||||  | |||||||||||| | ||||| ||||| ||  | || |||||||  |||     |   |     ||| |  |||   |||  |   ||||  | |   ||||| |  | ||    | ||   ||    |||          
ATCTTCAATGGTGTCTTCCTCAAGGTTAACAAGGCAACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtatgttatcaattttagctgctgttctgtttatatatttagctgtgctaattattgcttgctgttacagacttg-taatcc-tccatcgcaaattatcaat

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G178807_T03 (Zea mays), 5'ss of exon 4
--------------------ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgca-atctgattctctct-ctttcaataggattatgtaa-actaaactatatgctgctctaaaccgaatgatatatctggtgcag-----------
                    |||||||||||||| ||||| ||||| |||||||||||  | |||||||| ||  | || || ||||| ||  | || ||||| |    | | | | |  || |  | | |    || || |    |    |  ||  |     ||  |   ||      | | | ||            
AGCTCCTGCGTTTGAGGCAGATCTTCAATGGTGTCTTTCTCAAGGTTAACAAGGCAACTATTAACATGCTACGGAGGGTGGAGCCATATGTTGCGTATGGgtaagtttgtataaatttagctgccgtgagtgcatttttggagtgttgggatgcattttaacacaacactgctgtggctgccgcttcatcagttttgaga

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G23750.2 (Glycine max), 5'ss of exon 5
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttca-ataggattatgtaaactaaactatatgctgctctaaaccgaatgatatatctggtgcag
|| ||||||||||| ||||| || || ||||| || ||||| |||||||||| | ||||||| || || |||||||| |||||||   | |  ||| ||  | | |  ||   ||||||   |      | |||      ||||   || |  |   | || |  ||
ATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCCTATGTGACTTATGGgtatg---tttacttccctgccatacttatttaattatgattataggtttttataac-tgctaatgagacttctgcttttgttttag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G02270.1 (Glycine max), 5'ss of exon 5
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaactaaactatatgctgctctaaaccgaatgatatatctggtgcag
|| ||||||||||| ||||| || || ||||| || ||||| |||||||||| | ||||||| || || |||||||| |||||||  | ||  | ||     |    ||    |||  ||   | |  ||| |       |||   || |  |   | || |  ||
ATTTTCAATGGTGTATTTCTCAAAGTTAACAAAGCCACAGTGAACATGCTGCACAGAGTTGAGCCGTATGTGACTTATGGgtatgtcaacttttccttgtcttacttat----ttaaatacgatgatttatttttactgttaatgagacttctgcttttgttctag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 5'ss of exon 5
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaa-----ctaaact-atatgctgctctaaaccgaatgatatatctggtgcag---------
|| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | | ||| || |  |||||||| ||||| | | ||| | ||| |   |||   ||  ||  | ||||     || ||||  | |  |  || |   | |||| ||| | |  ||||          
ATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGATGAGCCTTGTGTGACTTATGGgtaagta-tcttactcttttgtttttcttaaaatcctataaaaagttctgaacttgtgtattattc-atttctaatg-tatttatattgcaaatattttag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 5'ss of exon 4
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaa----ctaaact-atatgctgctctaaaccgaatgatatatctggtgcag---------
|| |||||||| ||||||||||| |||||||| |||||| | |||||| ||| | | ||||| || || |||||||| ||||| | | ||| | ||| |   |||   ||  ||  | ||||    |||||||  |||  |  || |   | |||| ||| | |  ||||          
ATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGGgtaagta-tctcactcttttgtttttcttaaaatcctataaaaagtctaaacttgtatattattc-atttctaatg-tatttatattgcaaatattttag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S243_40V6.1 (Physcomitrella patens), 5'ss of exon 3
--------------------ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgc------aatctgattctctctctttcaataggattatgtaaactaaactatatgctgctcta---aaccgaatgatatatctggtgcag------------------
                    ||||||||||| |||||  | |||||||||||||| || || |||||| ||||| | ||||| ||||||||||| |||||||  |       ||||        |||  ||    | ||  |    ||   || | |||  |  |||    ||  || ||  |     | | |                    
AGCTATTAAGACTGAGGCAGATCTTCAATGGCGTGTTCATGAAGGTGAACAAGGCCACCGTGAACATGTTGCGCAGGGTTGAGCCATACGTGACGTACGGgtgagttggaaaaatcaccagtcttctggtttgtcacgagaaaagtaatggaaatgtattatcatctccacaattgattgcaacgatagttactaacccttatcattttccag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S7_369V6.1 (Physcomitrella patens), 5'ss of exon 3
--------------------ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaactaaactatatgctgctctaaaccgaa--tgatatatctggtgcag--------------------------------------------------------------------------
                    ||||||||||| || ||  | |||||||||||||| || || |||||| ||||| | ||||| |||||||| ||||| ||||  |     |   ||| |   |||    || |||      |  |   | ||    | |  ||| ||    | |   |   |||  |                                                                           
AACTGTTGAGGCTGAGGCAGATCTTCAATGGCGTATTCATGAAGGTGAACAAGGCTACCGTGAACATGTTGCGCAGGGTTGAGCCATACGTCACTTATGGgtgagttcgatatctctatggattttgtaagaattgaaggtagcatcat-tacttcgattgaaatcggcgtttagggaatcggtttaagaaaaccattgctaaacattgacttgggccgtacacagcagcaacacttattggacttcacttgttttattcag

upper sequence: AT2G44120.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S28_10V6.2 (Physcomitrella patens), 5'ss of exon 3
--------------------ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc--tgattctctctctttcaa-taggattatgtaaactaaactatatgctg-ctctaaacc-gaatgatatatctggt-gcag---------------------------------------
                    |||||||| || |||||  | |||||||||||||| || ||||||||| ||||| | ||||| || ||||| || |||||||  |  | |  |  | |||    |  ||| |||| ||             |     ||| || |||||  |  |  |  |  || | |||                                        
AGCTGTTGAGGCTGAGACAGATCTTCAACGGCGTGTTCATGAAGGTGAACAAGGCCACCGTAAACATGTTGCGCAGGGTTGAGCCTTACGTAACCTACGGgtgagtcaccatttgtactcgaagtgccaaataggcttggaattggcgtcttgctaactggctataaacttgtgtttttcagttgtttgcactgaacataaaactgacatcgccaccattattattttcag

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|124921547|gb|EH995154.1|EH995154
EST:     GCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: GCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|86036881|gb|DR332636.1|DR332636
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGA
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGA
EST: gi|86036876|gb|DR332631.1|DR332631
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACNNNACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|164030326|gb|ES124916.1|ES124916
EST:     GTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAAGGTTATG
genomic: GTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGA-GGTTATG
EST: gi|124996195|gb|EL068464.1|EL068464
EST:     GAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: GAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|164005672|gb|ES202986.1|ES202986
EST:     CATGCTGCGCCGAGTTGAACCANACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: CATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|163982594|gb|ES188968.1|ES188968
EST:     AACCATACGTGACTTACGG                         ATACCCAAACTTGAAGTAGCGTTAAGGAACTGATCTACAAAAGAGGTTATG
genomic: AACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAG-AGCGTTAAGGAACTGATCTACAAAAGAGGTTATG
EST: gi|164097943|gb|ES159694.1|ES159694
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGA
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGA
EST: gi|86036880|gb|DR332635.1|DR332635
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACATGACTTACGG                         ATACCCAAACTTGAA
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAA
EST: gi|86036879|gb|DR332634.1|DR332634
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|86036873|gb|DR332628.1|DR332628
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAA
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAA
EST: gi|86036877|gb|DR332632.1|DR332632
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTA
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTA
EST: gi|86036878|gb|DR332633.1|DR332633
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATC
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATC
EST: gi|164125169|gb|ES186458.1|ES186458
EST:     AACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: AACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
EST: gi|86036874|gb|DR332629.1|DR332629
EST:     AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGG                         ATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG
genomic: AAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatc ... tctggtgcagATACCCAAACTTGAAGAGCGTTAAGGAACTGATCTACAAAAGAGGTTATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTCAATGGTGTGTTTCTTAAGGTGAACAAGGCAACAGTAAACATGCTGCGCCGAGTTGAACCATACGTGACTTACGGgtatgcaatctgattctctctctttcaataggattatgtaaactaaactatatgctgctctaaaccgaatgatatatctggtgcag

- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - TGCTGC