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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg...

Basic information

species Arabidopsis thaliana
transcript AT3G04840.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g10340.1 (Oryza sativa), 5'ss of exon 4
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccc-tgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg
 ||| | ||||  ||  | || |||||||||| |||||||||| | ||  |||||||||| |||||||||||||| |||||| | || || ||| | ||||||    ||  | |    |    ||||  | | |     |   | ||    |||| |   | || |  ||||||  |   |   |||||||||  |  | |
AGACGGCTACATGCTGCGTCTGTTCTGTATCGGCTTCACCAAGCGGCGGCCTAACCAGGTGAAGAGGACTTGCTATGCTCAAGCGAGTCAGATCAGACAGgtaatttcatttccaaggtctcttactgattgatgtatattggtccactg-ttgagcagctgctatatttactgtctttga---ttgcaatct--gcccag

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 4
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg----
 || |  |||   ||  |  | ||||| || || ||||| || |   |  | |||||| | |||| ||||||||||||||||  |||||| |||||||||||  |||| |||  | || |     || | ||      |   ||  ||  ||  | |  | ||   ||        ||       ||  || |  | ||     
GGATAACTACCAGCTTCGCATTTTCTGCATTGCATTCACGAAAAAGAGGCCGAACCAGATTAAGAAGACTTGCTACGCTCAAAGCAGCCAGATCCGTCAGgtttgcactcatcgcacttcg----ttttcgtctcaatttcatagtgattttattttgatactggaatcgtcagtgccgtacaaggcgttcatgcaacttcgaa

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ09804 (Selaginella moellendorffii), 5'ss of exon 5
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggc-ctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg
 ||||  |||||  | ||||| ||||| || |  ||||||||  |  |  | |||||||| |||||||||||||||||||| || || || ||||| ||||||  |              || |     |||| | |  | | |||| ||| |  ||||   |                                      
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAACGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCAAGTCAGATCCGCCAGgtatacttg-----------aaaagaaagagttggccgttcattaca-aacatactctcgcacag------------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ11647 (Selaginella moellendorffii), 5'ss of exon 5
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg
 ||||  |||||  | ||||| ||||| || |  ||||||||  |  |  | |||||||| |||||||||||||||||||| || || || ||||| ||||||  |    |       | || | |||  ||      | | |||| ||| |  |||||  |                                      
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAACGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCAAGTCAGATCCGCCAGgtatacttgaaaa-----gaaagagttg--gtcg---ttcattaca-aacatcctctctcacag------------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 5
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg
 ||||  |||||  | ||||| ||||| ||||  ||||||||| |  |  | |||||||| |||||||||||||||||||| || || || ||||| ||||||| |    |       | || | |||  | |     | | ||   |||    |||| | |                                      
TGACAACTACACCTTGAGGCTGTTCTGCATCGGATTCACCAAGCGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCGAGTCAGATCCGCCAGgtacacttgaaaa-----gaaagagttg--gctg---ttcattaacaaacacactctcgtgcag------------------------------------

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ09763 (Selaginella moellendorffii), 5'ss of exon 5
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg
 ||||  |||||  | ||||| ||||| || |  ||||||||| |  |  | |||||||| |||||||||||||||||||| || || || ||||| ||||||| |           || ||     |   ||     | | ||   ||| || |||| | |                                      
TGACAACTACACCTTGAGGCTCTTCTGCATTGGATTCACCAAGCGGAGGCCCAACCAGGTGAAGAGGACTTGCTACGCTCAGTCGAGTCAGATCCGCCAGgtacac----------ttgaaaagaaagagtttgctgttcattaacaaacatgctctcgtacag------------------------------------

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|125111981|gb|EL163248.1|EL163248
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGA
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGA
EST: gi|116436618|gb|EG479210.1|EG479210
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|164233953|gb|ES145003.1|ES145003
EST:     GGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAACCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: GGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|124921369|gb|EH994993.1|EH994993
EST:     TCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: TCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|125112820|gb|EL163865.1|EL163865
EST:     TCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: TCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|163972009|gb|ES156360.1|ES156360
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         T
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcag-
EST: gi|163972009|gb|ES156360.1|ES156360
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         T
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcag-
EST: gi|125123102|gb|EL169551.1|EL169551
EST:     AGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGA
genomic: AGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGA
EST: gi|124940705|gb|EL017133.1|EL017133
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACAT
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACAT
EST: gi|125290597|gb|EL304682.1|EL304682
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACAT
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACAT
EST: gi|86081250|gb|DR377007.1|DR377007
EST:     CTAACCAGGTCAAGAGGACTT-STACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|164075431|gb|ES153215.1|ES153215
EST:     GCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: GCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|125152149|gb|EL183934.1|EL183934
EST:     AGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: AGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|124869609|gb|EH954046.1|EH954046
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATC
EST: gi|125029573|gb|EL101842.1|EL101842
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAG
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAG
EST: gi|116425121|gb|EG467713.1|EG467713
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|86077074|gb|DR372831.1|DR372831
EST:     ATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: ATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|116436720|gb|EG479312.1|EG479312
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|125292432|gb|EL306517.1|EL306517
EST:     AGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: AGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|124713186|gb|EH804588.1|EH804588
EST:     CTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: CTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|163989408|gb|ES064393.1|ES064393
EST:     AAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: AAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
EST: gi|125309129|gb|EL323214.1|EL323214
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGC
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGC
EST: gi|163976319|gb|ES169499.1|ES169499
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCT
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCT
EST: gi|164211200|gb|ES125546.1|ES125546
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAG
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAG
EST: gi|164160822|gb|ES136669.1|ES136669
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAA
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAA
EST: gi|124824555|gb|EH909421.1|EH909421
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGG
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGG
EST: gi|124819556|gb|EH904422.1|EH904422
EST:     CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCAT
genomic: CTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCAT
EST: gi|164124847|gb|ES167460.1|ES167460
EST:     GCCAAATCCGTCAG                         ATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC
genomic: GCCAAATCCGTCAGgtacgcacac ... aattcctcagATCCGCAGGAAGATGAGGGACATCATGGTTAGGGAAGCTTCCTCATGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACAGTTACACTCTCAGGCTATTCTGTATCGCCTTCACCAAGAGACGTGCTAACCAGGTCAAGAGGACTTGCTACGCTCAATCCAGCCAAATCCGTCAGgtacgcacacattcccctgcaatacttgtagttaggcctgactacagaacttgatctctttctcttattactgaatcctacttttgcaatctttgatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctct