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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttcttactgacaattctatgtgacctctaattacag

Basic information

species Arabidopsis thaliana
transcript AT1G43170.7
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 5'ss of exon 4
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagt---ttgcttattgaatggaagtgtatatcataaactcttctgc---actacgttcttactgacaattctatgtgacctctaattacag----------------------------
|    ||||||| || || |  ||||||||||  || ||    ||||||||||||||||||||||| ||| ||||  |||||||  | |  ||||||||||| |||    | ||  |    |   |   | |||  | | | |||||       ||  |   |  | || ||    ||| |  | |   | ||                             
TCTCAAGTATGATAGCGATGCCGGCAAGAAGGAAATCCAAATGCAGCTTGAGAAGATGAAGAAGTATGCTTCTGTTGTCCGTGTGATCGTGCACACTCAGgtcagtaacctactgttattttactatcttgtattttgagcccttctattcagttaattggatggtaaccatgtgctgtaaattgtttgttcattctcattctaaatctttatgtgcttcag

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G109677_T04 (Zea mays), 5'ss of exon 5
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttcttactga---------caatt-ctatgtgacctctaattacag--
|    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        |||  ||     | | |        |  |||||  |||         ||||| ||||  | | | || ||      
TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagcttaattgtgctttgttgttcattcatgattgtaggaacacagtttcttgatgattgatagtgcaattactattggtcttttatttggcttc

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G135727_T04 (Zea mays), 5'ss of exon 4
------------------------------------------------TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttcttactgacaattctatgtgacctctaattacag
                                                |    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        ||   ||   |   |  |  | || | ||                                   
CTACAAGAACTGGTGCAAGAGCAAGAAGAAGGCTTTCACAAAGTATGCTCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGaagatgaagaaatatgcttctgttatccgtgtcattgctcatacccaggtaagaagcttaattgtgctttgttgctcatt-catgtttgtaggaacaaagt-----------------------------------

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G135727_T03 (Zea mays), 5'ss of exon 4
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttctt-----actgacaattctatg-----tgacctctaattacag---
|    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        ||   ||   |   |  |  | || | |||  |     | ||| ||| | ||      ||  || | |||       
TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagcttaattgtgctttgttgctcatt-catgtttgtaggaacaaagtttcttaatgattgataatgcaattactcttggtcttttatttggcttc

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G324314_T05 (Zea mays), 5'ss of exon 4
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcac-tacgttcttactgacaattctatgtgacctctaattacag-------------
|    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        ||   ||   |   |  |  | ||  |  |||||| |||    |  |||  |   ||| |                  
TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagcttaattgtgctttgttgctcatt-catgtttgtaggaacacagtttcttaatgattgatg-atgcaattactattggtcttttatttggcttc

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G132968_T02 (Zea mays), 5'ss of exon 4
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttctt-----actgacaattctatg-----tgacctctaattacag---
|    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        ||   ||   |   |  |  | || | |||  |     | ||| ||| | ||      ||  || | |||       
TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagcttaattgtgctttgttgctcatt-catgtttgtaggaacaaagtttcttaatgattgataatgcaattactattggtcttttatttggcttc

upper sequence: AT1G43170.7 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 3
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcac-tacgttcttactgacaattctatgtgacctctaattacag-------------
|    | ||||| | ||| | |||||||||||  ||||||   |||||||||||||||||||| || ||| |||| ||||||||  | ||||| || ||||||||     | ||||        ||   ||   |   |  |  | ||  |  |||||| |||    |  |||  |   ||| |                  
TCTCAAATATGAAAATGATGCTGGCAAGAAGGAAATTCAGCTGCAGCTTGAGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagcttaattgtgctttgttgctcatt-catgtttgtaggaacacagtttcttaatgattgata-atgcaattactattggtcttttatttggcttc

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|163988357|gb|ES000958.1|ES000958
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATNAAGGGATTG
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTG
EST: gi|164115220|gb|ES061057.1|ES061057
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGA
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGA
EST: gi|86027147|gb|DR322900.1|DR322900
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|86027115|gb|DR322868.1|DR322868
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|116447558|gb|EG490150.1|EG490150
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|86027130|gb|DR322883.1|DR322883
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|124957451|gb|EL032286.1|EL032286
EST:     GAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
genomic: GAAGATGAAGAAGTACGCTACTGTCATCCGTG-TTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
EST: gi|86027196|gb|DR322949.1|DR322949
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|163989803|gb|EL990785.1|EL990785
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTG
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTG
EST: gi|164140722|gb|ES212910.1|ES212910
EST:     GTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGAATTGAAGCAGAAGAAGGCTCACAT
genomic: GTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGA-TTGAAGCAGAAGAAGGCTCACAT
EST: gi|47830691|gb|CK120375.1|CK120375
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|125246197|gb|EL260282.1|EL260282
EST:     TACGCTACTGTCATCCGTGTTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: TACGCTACTGTCATCCGTG-TTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|124892912|gb|EH971814.1|EH971814
EST:     GCTCACACTCAG                         ATCAGGAAGATTGAAGGGATTGAAGCAGAAGAAGGCTCA
genomic: GCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGA-TGAAGGGATTGAAGCAGAAGAAGGCTCA
EST: gi|47830713|gb|CK120397.1|CK120397
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|125098273|gb|EL154471.1|EL154471
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGG
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGG
EST: gi|86027195|gb|DR322948.1|DR322948
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAG
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAG
EST: gi|116447562|gb|EG490154.1|EG490154
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|164224958|gb|EL970886.1|EL970886
EST:     GAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATT
genomic: GAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATT
EST: gi|164056353|gb|EL970991.1|EL970991
EST:     GTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
genomic: GTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
EST: gi|47831476|gb|CK121160.1|CK121160
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|124866584|gb|EH951021.1|EH951021
EST:     CCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: CCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|116393945|gb|EG436537.1|EG436537
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAGGGCTCACATGATGGAGATC
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
EST: gi|164197790|gb|EL973939.1|EL973939
EST:     GTACGCTACTGTCATCCGNGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
genomic: GTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACAT
EST: gi|86027178|gb|DR322931.1|DR322931
EST:     AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGA
genomic: AGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGA
EST: gi|124709794|gb|EH801196.1|EH801196
EST:     GTGTTTTGGCTCACACTCAG                         ATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC
genomic: GTGTTTTGGCTCACACTCAGgtaagtttgc ... ctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGCAGTATGACAGTGAGGATGGCAAGAAGGGTATTCAGGCTCAGCTTGAGAAGATGAAGAAGTACGCTACTGTCATCCGTGTTTTGGCTCACACTCAGgtaagtttgcttattgaatggaagtgtatatcataaactcttctgcactacgttcttactgacaattctatgtgacctctaattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT