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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactattggcgttaggctctgtgttctgatctactatcttgtgatatccttctttag

Basic information

species Arabidopsis thaliana
transcript AT3G15660.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15660.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G44000.2 (Glycine max), 5'ss of exon 2
GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactattggcgttaggctctgtgttctgatctactatcttgtgatatccttctttag
||||| |||||||||||||||||||| |||||||||||||| ||||| | ||| |||||||| ||||| || || || || ||||| || || |||||| ||||||    |||          |  |||| |||        || ||   |  | ||  ||     ||    |      | || |  | |      | || | ||       
GATGTCAAGGATAATCCTGTTATGATTTACATGAAAGGTGTGCCTGATTTTCCACAGTGTGGATTTAGTTCTCTTGCAGTTAGAGTGTTACAACAATATGgtaagtaacattgtg----cacctataacttaagtgtagacttggga--ctgatataggataactattctattaaacactatggtgaattgatgattaatttgcta------

upper sequence: AT3G15660.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G22430.2 (Glycine max), 5'ss of exon 3
GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactattggcgttaggctctgtgttctgatctactatcttgtgatatccttctttag
||||| |||||||||||||||||| | |||||||||||||| ||||| | ||| || ||||| ||||| || || || || ||||||||  | || ||| ||||||  |      | |   |      |||  ||    ||   |   |||  ||  ||||    | |    ||   |     || |  ||   | |||  ||         
GATGTCAAGGATAATCCTGTTATGGTTTACATGAAAGGTGTGCCTGATTTTCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctctat----gatgaagtcgtagaagaaatttgttacagtatgaattca--------

upper sequence: AT3G15660.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G22430.1 (Glycine max), 5'ss of exon 3
GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactat--tggcgtt------aggctctgt---gttctgatctactatcttgtgatatcc-ttctttag--------------------------------
||||| |||||||||||||||||| | |||||||||||||| ||||| | ||| || ||||| ||||| || || || || ||||||||  | || ||| ||||||  |      | |   |      |||  ||    ||   |   |||  ||  ||||  ||  ||           | |||     | |||  |   |||   ||||| |  |||| ||                                 
GATGTCAAGGATAATCCTGTTATGGTTTACATGAAAGGTGTGCCTGATTTTCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctctatgatgaagtcgtagaagaaatttgttacagtatgaattcacatcacttgataacaattctgtaagttacaatcatcattatataatgctcttgcag

upper sequence: AT3G15660.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G03660.1 (Glycine max), 5'ss of exon 3
GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactat--tggcgtt----aggctctgtgttc-----tgatctactatcttgtgatatcc-ttctttag--------------------------------
||||| |||||||||||||||||| | |||||||||||||| ||||| | ||| || ||||| ||||| || || || || ||||||||  | || ||| ||||||  |      | |   |      |||  ||    ||   |   |||  ||   |||  ||  |||    | |   | ||||      |||  |   ||    ||||| |  |||| ||                                 
GATGTCAAGGATAATCCTGTTATGGTTTACATGAAAGGTGTGCCTGATTTTCCACAATGTGGATTTAGTTCGCTTGCTGTAAGAGTTTTAAAACACTATGgtaagtactaagttcaagacaagcttttctgttgatatttttgttctttttgtttctttatggtgaagttgtagaagaaatatgttagaatatgaattcacattacttgataacaattctgtaagttgcaatcatcattatataatgttcttgcag

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|164120538|gb|ES008520.1|ES008520
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTC
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTC
EST: gi|86075951|gb|DR371708.1|DR371708
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
EST: gi|19874734|gb|AU235565.1|AU235565
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
EST: gi|124972598|gb|EL046282.1|EL046282
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAAC
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAAC
EST: gi|86079164|gb|DR374921.1|DR374921
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAATTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
EST: gi|86081518|gb|DR377275.1|DR377275
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
EST: gi|19740939|gb|AU226292.1|AU226292
EST:     TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGGTTGAAAAAC
genomic: TCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGA-GTTGAAAAAC
EST: gi|125261988|gb|EL276073.1|EL276073
EST:     AGTTTTGCAGCAATATA                         ATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG
genomic: AGTTTTGCAGCAATATAgtaagttttg ... ccttctttagATGTTCCTATCAGTTCTAGAAACATTCTAGAAGACCAAGAGTTGAAAAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGAAGGATAATCCTGTTATGATCTACATGAAAGGTGTCCCTGAATCTCCTCAGTGTGGGTTTAGCTCACTAGCCGTCAGAGTTTTGCAGCAATATAgtaagttttgttgaaatgttgattgaaactgaagaagccttctgtgaattttctttactattggcgttaggctctgtgttctgatctactatcttgtgatatccttctttag

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