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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag

Basic information

species Arabidopsis thaliana
transcript AT4G14342.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttag-tgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag
|| || || ||||| ||||| |||||||| ||||||||||||||||| |||||||| || || || |||||||| |||| | |||||| ||| | | ||  |   |  |   ||||  | | | ||    |  | || |  ||  || | |   | |||  ||| | ||      
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagtatatctttttccaaaataaacaaaaatgtgt-tgttgggaatgtagtaact--tagtattgaggatttcttttattgcag---

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G121942_T03 (Zea mays), 5'ss of exon 3
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag
|| || |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  |||||||| ||| || | |  |||| ||    |||       ||||       ||||  |  |  |||   |    ||| ||       |||||
GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaag------atgctactaaattataagacatcaatgcttaattttgtttccttatttacag

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 3
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag
      |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  |||||||| ||| || | |  |||| ||    |||       ||||       ||||  |  |  |||   |    ||| ||       |||||
-----CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaag------atgctactaaattataagacatcaatgcttaattttgtttccttatttacag

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag
|| || ||||| || ||||| || ||||||||||||||||||||||| ||||||||||| || || ||||||||||||  |||||||| |||  | | |  |||| ||    ||   | |   || ||| | |    |  |  || | | ||     |  |||| |        
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaattatatgacattaccgcttaat-gttttccttatttacag-------

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag--------
|| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || |||||||||||||  |||||||||||||  | |   | |  |   ||| ||||| | |  ||| ||   | |   || |||| | |    |   ||     |||            
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctct--tccccaattttttttgttaatt-ttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 2
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaa-atttttatatgcattgtttttattggctactaatttgtggaattggtttaaatg-gtacag--------
|| ||||||||||||||||||||||| |||||||||||||| ||||| |||||||||||||| || ||||| |||||||  ||||||||||||||| |   | |   | |||   | |||| | |  ||| ||   |||   |  |||    | |  ||  |||   || ||            
GCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATTgtgagtttctctctctctcccttttccccaattttttgtttatttttaaaattatttgttaaccgtttgtttttctttgtgtgcgtgtgtgtgtgcag

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattg--gtttaaatggtacag
|| |||||||||||||| || || || |||||||||||||| ||||| |||||||||||||| ||||||||||| |||| |||||||| |||  | | | |||||||  ||    || | ||   |||| | ||||| || |  |  ||  | || |||  ||||     |  |||
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagattt--ggttgtcat---cattttatttataggtttttctttcttagatttgatgttttgtgtgggcag

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|86025219|gb|DR320972.1|DR320972
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025225|gb|DR320978.1|DR320978
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|47828971|gb|CK118655.1|CK118655
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025228|gb|DR320981.1|DR320981
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTNNATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025223|gb|DR320976.1|DR320976
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025236|gb|DR320989.1|DR320989
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025218|gb|DR320971.1|DR320971
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTNSATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025217|gb|DR320970.1|DR320970
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTNGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025230|gb|DR320983.1|DR320983
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTMGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025215|gb|DR320968.1|DR320968
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTMRATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025220|gb|DR320973.1|DR320973
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025231|gb|DR320984.1|DR320984
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTARATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025222|gb|DR320975.1|DR320975
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTVGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACWTTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025234|gb|DR320987.1|DR320987
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTRGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025229|gb|DR320982.1|DR320982
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025232|gb|DR320985.1|DR320985
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTNSATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|125201463|gb|EL216417.1|EL216417
EST:     GGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: GGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025233|gb|DR320986.1|DR320986
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025226|gb|DR320979.1|DR320979
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTWGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
EST: gi|86025221|gb|DR320974.1|DR320974
EST:     CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT                         TGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA
genomic: CATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttct ... aatggtacagTGAGTGGGCTGTGAACATTCAGCGTGATAGTTATGCTTCATACATTGGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattggtttaaatggtacag

- - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT