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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattataaccgtagtttgacatagcacaatttattttagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag

Basic information

species Arabidopsis thaliana
transcript AT1G21065.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 5
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattataaccgtagtttgacatagcacaatttattttagcttttggatgtt-cacttaacaagtgtttgttcattttggtctgcag
| ||||||||||||||||| ||||| || |||||||||||||| |||   || ||||  |        |     ||       ||   |||  ||   ||      ||       |      | | ||  ||  | |  |  |      || |||
GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGACgtatgtgttccctaatccctacattcttttccccatgtcaattttctcccaagtgagccaacaaaatattaaattagattcttcttttgcattgcttcag

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G141241_T03 (Zea mays), 5'ss of exon 3
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACT----CACgtgagctacaatcatattata-accgtagtttgacatagcacaatt-tattt-tagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag
| ||||||||||||||||| |||||||| |||||||||||||| |||   ||     | ||   || |  ||||  | |  |      |||||  |  |  | || ||||| || |  ||||    |  | | |                           
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatgtagactcctttcatcctttccattaacttttgatgtgtccaagttatatttataacacttggtctattgcctcat--------------------------

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM5G890647_T02 (Zea mays), 5'ss of exon 3
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattataaccgtagtttgacatagcacaatttattttagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag
| ||||||||||||||||| |||||||| |||||||||||||| |||   || | ||  | || | || | | ||  |  |   || || |      || | |   || |     || || |  |||||  || |   |    |  |       
GACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGATgtatg-tagactcctttcatc-ctttccattaacttt---tgatgtgtccaagtt-----atattta--taacacttggtctattgcctcag-------

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 5
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattata-accgtagtttgacatagc-acaatttattttagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag
| || |||||||||||||||||||| || ||||| |||||||| |||  |||||||||||| | | |   ||| |  |   |  |||  |||    | || ||||  ||   ||  ||  | |    | |   | ||| | | ||||         
GGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCACgtgagcaatacttccatttttcagtttgatttatcatgctgaaaagttatggtaatgttatgaactactggcatcttatatttttacttttttag------

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|164162025|gb|EL985428.1|EL985428
EST:     GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGGAAAACTCAGCA
genomic: GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGGAAAACTCAGCA
EST: gi|86078659|gb|DR374416.1|DR374416
EST:     GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAG
genomic: GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAG
EST: gi|124795012|gb|EH884691.1|EH884691
EST:     GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGGAAAA
genomic: GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGGAAAA
EST: gi|164216158|gb|ES058977.1|ES058977
EST:     GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGG
genomic: GATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGG
EST: gi|125223979|gb|EL238064.1|EL238064
EST:     TGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAGGGAATATG
genomic: TGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAGGGAATATG
EST: gi|164235466|gb|ES093209.1|ES093209
EST:     GCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC                         AATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAG
genomic: GCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctaca ... tggtctgcagAATCCCAATAACAAAAGGAAAACTCAGCATGGGAACTTGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCACgtgagctacaatcatattataaccgtagtttgacatagcacaatttattttagcttttggatgttcacttaacaagtgtttgttcattttggtctgcag

- - - - - - -  CAGCTC
- - - - - - - - AGCTCA