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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGGGCATCAAAGATCCGCAAGTTGTTTAACCTTGGAAAAGAGGATGATGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcag

Basic information

species Arabidopsis thaliana
transcript AT5G10360.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 5'ss of exon 5
AAGAGGGCATCAAAGATCCGCAAGTTGTTTAACCTTGGAAAAGAGGATGATGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaag-------aaaattagattcacttaaagagataattgaaaactgtttatacgattga-tgatttactaatatatgaggcttccatgtgcag-----
||||||||||| |||||| | ||| ||||||||||||  || || ||||||||  | ||||| || |||||||||||| | |||||||| | |||||| ||| ||       || ||| | |         ||| |  ||    | | | | |    | || ||  ||       | ||  ||||   |   ||      
AAGAGGGCATCTAAGATCAGGAAGCTGTTTAACCTTGCCAAGGATGATGATGTCCGCAAGTATGTCAACACTTACCGCAGAACCTTCACTACCAAGAACGgtgagcattcctaacattcggtattaaccttgagttgctttgctattatgtttgttgtggactgcattgtatgcctctggtgcttgtgtaatcaacacaa

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G09330.1 (Glycine max), 5'ss of exon 3
AAGAGGGCATCAAAGATCCGCAAGTTGTTTAACCTTGGAAAAGAGGATGATGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaattagattcacttaaagagataattgaaaactgt-ttatacgattgat--gatttact----aatatatgaggcttccatgtgcag--------
||||| ||||| || ||||| |||||||| |||||    || || ||||||||||||||||| || ||||| ||||| || ||||||||||  ||    |||||  |  ||   |   ||   | |  |   |      | | | ||  |||  |    |  | |     |||| || |||      ||   |         
AAGAGAGCATCCAAAATCCGTAAGTTGTTCAACCTGTCTAAGGAAGATGATGTGAGGAAGTATGTCAACACATACCGTCGAACCTTCACAACAAAAGTTGgtaa--agtttcattgtgctagtatatttgccttttggttttgtcatttgatgtacccaacctgccatcaaatagataagggggaggtggatattttataat
















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|164064661|gb|EL997996.1|EL997996
EST:     GAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCC
genomic: GAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCC
EST: gi|125196219|gb|EL211173.1|EL211173
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAG
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAG
EST: gi|124986967|gb|EL059452.1|EL059452
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTC
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTC
EST: gi|116420456|gb|EG463048.1|EG463048
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|164192909|gb|ES074012.1|ES074012
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCC
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCC
EST: gi|124820853|gb|EH905719.1|EH905719
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGAT
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGAT
EST: gi|86082185|gb|DR377944.1|DR377944
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|124716461|gb|EH807863.1|EH807863
EST:     AGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAGCAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: AGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|163992739|gb|ES137598.1|ES137598
EST:     GTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: GTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|116414309|gb|EG456901.1|EG456901
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|164150491|gb|ES197728.1|ES197728
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGC
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGC
EST: gi|164024371|gb|ES146996.1|ES146996
EST:     TACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|86080275|gb|DR376032.1|DR376032
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|86076579|gb|DR372336.1|DR372336
EST:     GTGAGGAAGTNACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: GTGAGGAAGT-ACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|124906639|gb|EH980719.1|EH980719
EST:     ACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCTGAGGCTTGTGACTCCATTGA
genomic: ACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
EST: gi|47830707|gb|CK120391.1|CK120391
EST:     TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGG                         GCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA
genomic: TGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaat ... ccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGGGCATCAAAGATCCGCAAGTTGTTTAACCTTGGAAAAGAGGATGATGTGAGGAAGTACGTTAACACTTACCGCCGTACCTTCACAAACAAGAAGGgtaagaaaattagattcacttaaagagataattgaaaactgtttatacgattgatgatttactaatatatgaggcttccatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG