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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtttaaagtgaactggagtcactgttgttgagtgtctctttttttactaattaatgccgttgccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG

Basic information

species Arabidopsis thaliana
transcript AT2G03120.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtttaaagtgaactggagtcactgttgttgagtgtctcttttttta------ctaattaatgccgttgccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
  || | |  |||   | | | |  ||| | |   |   | || | | ||  ||||| ||   || |||         ||   |      | |  |        |   ||          ||| || || |  ||     ||||||||||||||||||| || || ||||||||||| |||||||| || || |||
-gta-tgcttttgtgttattttgagatata-aggttaatatgcattattgaaataac-tatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 6
gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtt-taaagtgaactggagtcactgttgttgagt-gtctctttttttactaattaatgccgttgccaat-acagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
                                 | |||   | |||  || | | |    || |||  |   ||  |||||    |||     ||  | |   || | |        |   ||      ||  || | |||||||||||| ||||| ||||| || || |||||||||||||| || || |||
---------------------------------attctatcgtttc--tgctgtga----atgtttgtgcaatactgtgaatc--agttttgattactaaacagtatttgacaccgatggcta-catatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG

upper sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 6
gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtttaaagtgaactg-gagtcactgttgttgagtgtctctttttt--tactaattaatgcc--gttgccaat-acagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
                                               || | |||  ||  |||  | ||||       |||| || ||| | ||| | | |      | |||   ||  || | | |    ||  || | |||||||||||| ||||| ||||| || || |||||||||||||| || || |||
--------------------------------------------attctatcata-tatgctatgaatgtttgtgtaatactgtgaatcatttttgattactagacagtatttaacaccgatgactacatatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG

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|124956607|gb|EL031513.1|EL031513
EST:     AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAG                         GGAATTGAGATGCTCTCTCTCGGATCATTCAAGA
genomic: AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAGgttacttccc ... gccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGA
EST: gi|116442939|gb|EG485531.1|EG485531
EST:     AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAG                         GGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
genomic: AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAGgttacttccc ... gccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
EST: gi|86050556|gb|DR346311.1|DR346311
EST:     AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAG                         GRAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTG
genomic: AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAGgttacttccc ... gccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTG
EST: gi|86050550|gb|DR346305.1|DR346305
EST:     AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAG                         GGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
genomic: AAAAACATTGGCTGGCTAACAATATCCTCGGCCTTTCCTTCTGCATTCAGgttacttccc ... gccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
EST: gi|124947402|gb|EL023243.1|EL023243
EST:     AACAATATCCTCGGCCTTTCCTTCTGCATTTCAG                         GGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTT
genomic: AACAATATCCTCGGCCTTTCCTTCTGCA-TTCAGgttacttccc ... gccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcactgttgttgagtgtctctttttttactaattaatgccgttgccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG
                  tctctttttttactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtttaaagtgaactggagtcactgttgttgagtgtctctttttttactaattaatgccgttgccaatacagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG

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