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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctctatttggctggcttctcaatttactgatttggtgcttaagttgatcatttttgttgttgtggaatttcag

Basic information

species Arabidopsis thaliana
transcript AT1G21065.1
intron # 3
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 3
lower sequence: GRMZM2G092988_T04 (Zea mays), 5'ss of exon 2
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatc-tctatttggctggcttctcaatttactgatttggtgcttaagttgatcatttttgttgttgtggaatttcag
| || |||||||| || || ||||| ||||| ||||| |||||  | ||||| |||||||| |||||||||||  | ||||| |||||||| |||||   |   |||  |   |  ||||||  || | || |    |    | | || |   || |||  | ||    ||||||
TTCAGCACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAGgtcagtggcctaaatttttctcttctcttttaaatgctacaattaaaatgctgcttcgttatgtcatcgt----tttcag

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G092988_T01 (Zea mays), 5'ss of exon 2
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatc-tctatttggctggcttctcaatttactgatttggtgcttaagttgatcatttttgttgttgtggaatttcag
     |||||||| || || ||||| ||||| ||||| |||||  | ||||| |||||||| |||||||||||  | ||||| |||||||| |||||   |   |||  |   |  ||||||  || | || |    |    | | || |   || |||  | ||    ||||||
-----CACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAGgtcagtggcctaaatttttctcttctcttttaaatgctacaattaaaatgctgcttcgttatgtcatcgt----tttcag

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G17340.1 (Glycine max), 5'ss of exon 3
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgt--atatctctatttgg--ctggcttctcaatttactgatttggtgcttaagttgatcatttttgttg--ttgtggaatttcag---------------
| || ||||||||||||||||| || |||||||||||||||||    ||||||| || |||||| || || ||| | ||  |||| ||||| |||||  || | | ||||| |  ||  | |    |||||  ||   | |     | || |   ||  || |   || | |||||  |                
TGCATCACACAAGTGCTTCTCTTACCATCAATGAGAATTATGACTATGATGTTCGGGATGATACAGAAACCTTCCTCAATGGGATAGTTCCAGAGgttaatttttttatttagttcttacattaatatttatggaaaggtttaaatattttaaggttactgataaattattgaattctattctggatctctaata

upper sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 3
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctctatttg--gctggcttc-tcaatttactgatttggtgcttaagt-tgatcatttttgttgttgtggaatttcag--------------------
| || ||||| ||||||||||| || |||||||||||||||||  |||||||||  |  ||||| || || ||| | ||  |||| ||||| ||||| | | ||| | |    |    ||  |  ||| | |  |   || ||   || | |  |  | |  |  | |  | |||  |                    
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgttaatgtctcgggcag

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|125046330|gb|EL118599.1|EL118599
EST:     ATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATACTATGGAAGGTCCTGATG
genomic: ATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAGGTCCTGATG
EST: gi|116377495|gb|EG420087.1|EG420087
EST:     CACATGTTCAGGCTGATACTGACACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
EST: gi|86078659|gb|DR374416.1|DR374416
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
EST: gi|124980342|gb|EL053301.1|EL053301
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATA
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATA
EST: gi|116377317|gb|EG419909.1|EG419909
EST:     CACATGTTCAGGCTGATACTGACACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
EST: gi|125162823|gb|EL189593.1|EL189593
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGC-CCTTGGAGGCATACTATGGAAG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
EST: gi|86028440|gb|DR324193.1|DR324193
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCATACTATGGAAG
EST: gi|124933671|gb|EL010809.1|EL010809
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTACAGCGCCTTGGAGGCATACTATGG
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATT-CAGCGCCTTGGAGGCATACTATGG
EST: gi|116422128|gb|EG464720.1|EG464720
EST:     CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAG                         GGGAATTCAGCGCCTTGGAGGCAT
genomic: CAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctct ... ggaatttcagGGGAATTCAGCGCCTTGGAGGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctctatttggctggcttctcaatttactgatttggtgcttaagttgatcatttttgttgttgtggaatttcag

- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT