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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacacacccaaagatttcaatacaaagacaaaaacacgtaatggttgaaatgtgttcccag

Basic information

species Arabidopsis thaliana
transcript AT3G63140.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os07g11110.1 (Oryza sativa), 5'ss of exon 4
AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaag-tctctcaca--cacccaaagatttcaatacaaagacaaaaacac-----gtaatggt-tgaaatgtgttcccag--------------------
|||||| | || ||    ||||| | |||||| || || || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||| ||||  || | || |  | |||||  |  |     ||||    ||| | |       ||   | |  ||| ||    ||                     
AAGTACATCGCGGAGCAGTTCGGCAGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaaaatcacccaaatccccccaaccaaattctcccaaatttcaaaccgccccaaacaacattcttcaatttgaagacaaaattgtcaatttttttactg

upper sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
AAGTACTTAGCCGAAACATTCGGGAACTG---GGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacacacccaaagatttcaatacaaagacaaaaacacgt----aatggttgaaatgtgttcccag--------------
   ||| | || ||    ||||| | |||   ||| || || || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||| |||| |      | || ||   ||||      ||          | | |     | |      | |   |||  |              
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa-taaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag

upper sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaag------tctctcacacacccaaagatttcaa-tacaaagaca---aaaacacgtaatggttgaaatgtgttcccag-------------------
|| ||| | |  ||||| |  || |  |||||    || || || ||||||||||| || |||||||||||||||||||| || || ||||| || ||| |||||      | ||| | |||  |     | | || |  ||| |||    || |      |   | || ||   | | |                    
AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg

upper sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv07s0104g00510.t01 (Vitis vinifera), 5'ss of exon 4
AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacac-acccaaagatttcaa--tacaaagacaaaaacacgta-atggttgaaatgtgttcccag-------------------------
|  ||| |  | ||    ||||| | ||||||    || || |||||||||||||| || ||||| ||||||||||| || || || |||||||| |||||||||    | ||    | ||  | ||| ||  |      ||| |    | |  ||  |  ||||    | |||                          
ACATACATTTCAGAGGTTTTCGGCAGCTGGGCAATTTTCCGTCCGCAGTACATGATTGGATCTGGAAACAACAAAGATTGTGAGGAGTGGTTCTTTGACCgtaagcgaataaccttgcgcattggtttgaactttttgtaacacagctgcattcatcttcaaaatcccctgccattttcacattgatccgctctgaacag

upper sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S55_140V6.1 (Physcomitrella patens), 5'ss of exon 4
AAGTACTTAGCCGAAACA---TTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacacacccaaagatttcaat-acaaagacaaaaacacgtaatggt----tgaaatgtgttcccag-------------------------------
   ||  | || |||      || | |  ||||||||| || ||||| |||||||||| |||    || |||||||| || ||||||||||||||||||||| || ||| | | | ||   |     |     | || |||   ||     | || | |     || | ||||   |||                               
---TATCTGGCGGAATTGGGCTTAGAGTCCTGGGCCTCATTCCGACCTCAGTACATGACCGGAGACGGGAACAACAAGGATTGCGAAGAATGGTTCTTCGACAgtgagtattttaaaccttcgtctttcatgttcaccaagttcaatctctggaaagctacttcgataagtgtggtcagtggtagctcatgttgagtcgaaattttacag

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|125208150|gb|EL223104.1|EL223104
EST:     GAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
genomic: GAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
EST: gi|124818791|gb|EH903657.1|EH903657
EST:     GGCAACAACAAAGACTGCGAAGAATGGTTCTTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTA
genomic: GGCAACAACAAAGACTGCGAAGAATGGTTC-TTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTA
EST: gi|116429981|gb|EG472573.1|EG472573
EST:     TCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
genomic: TCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
EST: gi|116456654|gb|EG499246.1|EG499246
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAG
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAG
EST: gi|124891971|gb|EH970873.1|EH970873
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGA
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGA
EST: gi|124835516|gb|EH919955.1|EH919955
EST:     GACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
genomic: GACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
EST: gi|124738213|gb|EH829615.1|EH829615
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAG
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAG
EST: gi|164071843|gb|ES038877.1|ES038877
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACGGAGCAGTGCCAATCCCAGGATCAGG
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGG
EST: gi|125310059|gb|EL324144.1|EL324144
EST:     CGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGACTA
genomic: CGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAG-CTA
EST: gi|124931495|gb|EL008847.1|EL008847
EST:     CAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
genomic: CAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
EST: gi|47830467|gb|CK120151.1|CK120151
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATCCCAGGATCAGGATTGCAGCTAA
EST: gi|125251219|gb|EL265304.1|EL265304
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCA
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCA
EST: gi|125231247|gb|EL245332.1|EL245332
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATC
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATC
EST: gi|124978556|gb|EL051716.1|EL051716
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGA
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGA
EST: gi|124935960|gb|EL012904.1|EL012904
EST:     CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACC                         GGATTGTGAGGGACAGAGCAGTGCCAATC
genomic: CATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctct ... gtgttcccagGGATTGTGAGGGACAGAGCAGTGCCAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacacacccaaagatttcaatacaaagacaaaaacacgtaatggttgaaatgtgttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA