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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctctcacatgtgatctgagtagcttgataaacacatttctagatttgttctaattggtggatgttttaatttaag

Basic information

species Arabidopsis thaliana
transcript AT4G40040.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G40040.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G176358_T01 (Zea mays), 5'ss of exon 2
---------------ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctc--tcacatgtgatctgagtagcttgataaacacatttctagatttgttctaattggtg-gatgttttaatttaag
               ||||| ||||| ||||| || ||||| ||||| |||||||||||||||||||||||||| || |||||||||||  |    | | ||  |    ||||     || | | || |  |||||  |   | ||  |    |||   | | || ||| |      
GACATCATTTGCTAGATGGCGCGTACCAAGCAGACCGCTCGCAAGTCCACTGGAGGAAAGGCTCCTAGGAAGCAACTCGCTACAAAGgttcgttaggtgttccttttagtgtgcctacagaaccatgctttacacaactgatggttgataaacattatggtgttgctttgacag---

upper sequence: AT4G40040.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv00s2837g00010.t01 (Vitis vinifera), 5'ss of exon 2
ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctctcacatgtgatctgagtagcttgataaacacatttctagatttgt-tctaattggtggatgttttaatttaag
||||||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| || || || |||||    |  |   | |    | |  |||| |||  ||  | |  | |  | | | ||  | | |   || |  || || |  || |  
ATGGCTCGTACCAAGCAAACTGCTCGTAAGTCCACGGGAGGAAAGGCTCCTAGGAAGCAACTCGCGACCAAGgtg---cgtgctttttttttttttttctgtgtatgtttctgattataaattttggttgttgtgtttctgatttatattgttcttcag-

upper sequence: AT4G40040.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S3_368V6.1 (Physcomitrella patens), 5'ss of exon 2
-------ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctctcac-atgtgatctgagtagcttgataaacacatttctagatttgttctaattggtggatgttttaatttaag-------------------------------------------------------------------------
       ||||| ||||| ||||| ||||| ||||| ||||| ||||| || ||||| ||||||||||| || || ||||||| |    |||   | | || |   ||| || |||     | ||| |  ||   |      ||| || |  ||| |    ||| ||                                                                         
TTTCACAATGGCACGTACCAAGCAGACAGCCCGTAAATCTACCGGAGGTAAAGCTCCCAGGAAGCAGCTGGCCACCAAGgtaaca---aggcgtacgctatttttgctgtgtcgct--gccatcacgtaactttgtacagcataaatgctaaatgata-gctttgagagatggccaaggtatgctgtgattgcgaacgtgcacagatgacatatgtttgaattgggttcacataattcag

upper sequence: AT4G40040.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ13396 (Selaginella moellendorffii), 5'ss of exon 1
-----ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctctcacatgt-gatctgagtagcttgataaacacatttctagatttgttctaattggtggatgttttaatttaag
     ||||| ||||| ||||| || ||||| ||||| || ||||||||||| || ||||||||||| || ||||||||  | |||   |||     ||| |||  |    | ||     ||     ||| |   | |||                         
CTACAATGGCGCGTACCAAGCAGACCGCTCGCAAGTCCACCGGAGGAAAGGCGCCCAGGAAGCAGCTCGCCACAAAGgtttgtctctccctccagattgtcgattcggcctggtt--ctgacgatcgtctcggccttttcag-----------------------

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|164225760|gb|EL973665.1|EL973665
EST:     GGAAGCAGCTTGCT-CAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: GGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|116468465|gb|EG511057.1|EG511057
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|301503181|gb|HO208721.1|HO208721
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|164030187|gb|ES015143.1|ES015143
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|164087192|gb|ES016043.1|ES016043
EST:     TCGTAAGTCTACTGGAGGAAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: TCGTAAGTCTACTGGAGG-AAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|301501157|gb|HO206697.1|HO206697
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124742252|gb|EH833414.1|EH833414
EST:     CCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|116447859|gb|EG490451.1|EG490451
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124766631|gb|EH856761.1|EH856761
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCAACCAAACCACTGGAGGAGTCAAGAAGCCCCATC
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCA-CCAA-CCACTGGAGGAGTCAAGAAGCCCCATC
EST: gi|164089651|gb|ES196147.1|ES196147
EST:     GTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCC-ATCGT
genomic: GTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124943419|gb|EL019601.1|EL019601
EST:     CAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|116483084|gb|EG525676.1|EG525676
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124881290|gb|EH960192.1|EH960192
EST:     CTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|152035605|gb|BP859103.2|BP859103
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124925219|gb|EL003232.1|EL003232
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCA
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCA
EST: gi|164104439|gb|EL975105.1|EL975105
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAG
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAG
EST: gi|116427491|gb|EG470083.1|EG470083
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|124714510|gb|EH805912.1|EH805912
EST:     TTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCA
genomic: TTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCA
EST: gi|47829096|gb|CK118780.1|CK118780
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|125225278|gb|EL239363.1|EL239363
EST:     CGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|125274699|gb|EL288784.1|EL288784
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|125229303|gb|EL243388.1|EL243388
EST:     CCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|125021358|gb|EL093627.1|EL093627
EST:     CTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|164080421|gb|ES077787.1|ES077787
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAA-G                         GCTGCACGTAAGTCTGCACCAACCAC
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCAC
EST: gi|164187715|gb|ES003803.1|ES003803
EST:     GTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACC
genomic: GTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACC
EST: gi|116468466|gb|EG511058.1|EG511058
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|301501881|gb|HO207421.1|HO207421
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|116390647|gb|EG433239.1|EG433239
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|47830179|gb|CK119863.1|CK119863
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|125085420|gb|EL145265.1|EL145265
EST:     AGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: AGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|116427493|gb|EG470085.1|EG470085
EST:     CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
genomic: CTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT
EST: gi|164214904|gb|ES035339.1|ES035339
EST:     GGAAGCAGCTTGCTACAAAG                         GCTGCACGTAAGTCTGCACCAACCACTGGAGGAGCCAAGAAGCCCCATCGT
genomic: GGAAGCAGCTTGCTACAAAGgtaagactcg ... ttaatttaagGCTGCACGTAAGTCTGCACCAACCACTGGAGGAGTCAAGAAGCCCCATCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCTAGGAAGCAGCTTGCTACAAAGgtaagactcgggctctcacatgtgatctgagtagcttgataaacacatttctagatttgttctaattggtggatgttttaatttaag

- - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT