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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTTTGCAGCATATGAAAAGAAGTACCCAGAGGAAGCTTCTGAGTTGAAATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaactctctttgcattctgtacaattcaattggtattctagatatgagttatagaacatctttctttttccttttttag

Basic information

species Arabidopsis thaliana
transcript AT3G60750.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G38720.1 (Glycine max), 5'ss of exon 6
AAAGTTTGCAGCATATGAAAAGAAGTACCCAGAGGAAGCTTCTGAGTTGAAATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtaga------actctctttgcattctgtacaattcaattggtatt----ctagatatgagttatagaacatctttctttttccttttttag----
 |||||||||| |||||| ||||| |||   ||||||||| | ||| ||||  ||||||| |||||||||||||| ||||| |||||||| || || || || |||| |      |   ||   |  |    ||  ||| | |  |   |    ||   ||| ||||  |  |  |||       |  | ||   |    
CAAGTTTGCAGAATATGAGAAGAAATACAGTGAGGAAGCTGCAGAGCTGAAGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaactaacaaacttccaggtttctcttaatatttattctgggctaaatctccttattagttgaatgatgtctaatccaattttattggtgccct

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA03G03200.1 (Glycine max), 5'ss of exon 6
AAAGTTTGCAGCATATGAAAAGAAGTACCCAGAGGAAGCTTCTGAGTTGAAATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa-ctctctttgca----ttctgtacaattcaattggtattctagatatgagttatagaacatctttctttttcctt--ttttag-----------------------------------------------------------------------
 |||||||| |  ||||||||||| |||   ||||| ||| | || |||||||||||||||| ||||||||| |||||||| |||||||| || || || || |||| |  ||    |  ||    ||   ||||  |   |   | ||| || | ||  ||| | |  |||     ||   | |  ||| ||                                                                       
TAAGTTTGCTGAGTATGAAAAGAAATACAAGGAGGAGGCTGCAGAATTGAAATCTATTATCAATGGTGAATTCCCTGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaattctaaactcacaggtttttcttacatgtttgtaacttttcaaggtttggattacatactatccaaagttgatcatgatttcagtttgatttggtagtatggggcttcaaaaagttattccaaatattaaaacctggcttccaatttgatttcag

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 5'ss of exon 6
AAAGTTTGCAGCATATGAAAAGAAGTACCCAGAGGAAGCTTCTGAGTTGAAATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtag------aactctctttgcattctgtacaattcaattg---gtattctagat--atgagttatagaacatctttctttttccttttttag--------------------------------------------------------------------------
  ||||||| | ||| |||   |||||   ||| |||||| | |  ||||| ||| | |||| ||||||||||||||| || ||||||||||| || || ||||||||      || | | |  |  |||| | |||||  |||     | || ||| |  |||     | | | || || | |||     | || |                                                                          
CCAGTTTGCTGAATACGAACGCAAGTATAAAGAAGAAGCTGCAGTATTGAAGTCTCTCATCAATGGTGAATTACCTGCAGGTTGGGAGAAGGCACTTCCGgtaagtagtgatttaattgtttcggttttctttgcaattttatttttcattttttagttttatggtcatttggaaattttgcatttggacatatttgaaaatgtcaatacggatgctgttatatattggaatatagatgatttttaaggtaattttcttgctttgatatag

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|124814889|gb|EH899755.1|EH899755
EST:     AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACC
genomic: AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACC
EST: gi|47829115|gb|CK118799.1|CK118799
EST:     CTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
genomic: CTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
EST: gi|116446637|gb|EG489229.1|EG489229
EST:     AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
genomic: AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
EST: gi|124830582|gb|EH915028.1|EH915028
EST:     AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACCAG
genomic: AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACCAG
EST: gi|164225638|gb|ES046526.1|ES046526
EST:     CACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
genomic: CACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAA
EST: gi|124821378|gb|EH906244.1|EH906244
EST:     AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCT                         ACATACACACCAGAGTCTCCAGG
genomic: AATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaa ... ccttttttagACATACACACCAGAGTCTCCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTTTGCAGCATATGAAAAGAAGTACCCAGAGGAAGCTTCTGAGTTGAAATCTATTATCACTGGTGAATTACCTGCTGGCTGGGAGAAGGCTCTACCTgtaagtagaactctctttgcattctgtacaattcaattggtattctagatatgagttatagaacatctttctttttccttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA