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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag

Basic information

species Arabidopsis thaliana
transcript AT2G05990.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 10
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag
| ||  ||||||||||||| || |||||||| || ||||| |||||||||||||| |  | | || | || |     | |  |     ||    |||    || | |   |     ||| ||  |||  |   |||   | ||    | |||
GTGGATCTTCAATATCTCTGACATACATTGCTTCAGAAAGGATCATTCCTGGgtatg--ttggttatgcatagaaagtcctta----taattctatgttt-cataaatttagactgaca-atattcatga---tctaaataatg--atacag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 8
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag-
  ||  || |||| |||||||| |||||||| || ||||| |||||||||||||  |   |   |  |   || |   ||| |   |   | |  |      ||||  |  | |  |||   | |   || |  |||         |||||| 
-TGGATCTGCAATTTCTCTTACATACATTGCTTCAGAAAGGATCATTCCTGGGtgtgttggatatgctttaaaatc--tcatacatatttatttttat---tacattcctttattgacaaggttttg-aaatgcctcga-------gtgcaga

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 9
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag
| ||  ||||||| ||||| || |||||||| || ||||| ||||||||||||||    ||| |    || |     | |  |     ||    |||    || | |   |     ||| ||  |||  |   |||   | ||    | |||
GTGGATCTTCAATCTCTCTGACATACATTGCTTCAGAAAGGATCATTCCTGGgtattt-tggttatgccatagaaagtcctta----taattctatgttt-cataaatttagactgaca-atattcatga---tctaaataatg--atacag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 9
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacac-acataacgatgtcaacacattctcacaagtatctctttcattctgtgcag
  ||  || |||| |||||||| |||||||| || ||||| |||||||||||||  |   |   |  |   || |   ||| |   |||   | ||    |  ||||     | |  |||   | |   ||   |  |||  || | |     
ATGGATCTGCAATTTCTCTTACATACATTGCTTCAGAAAGGATCATTCCTGGgtgtgttggatatgctttaaaatc--tcatat--acatgtttatttttattacattcttttattgacaaggttttgaaa---tgccttatatgcag-----

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 5'ss of exon 9
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag
| ||||||||||| ||||| || ||||||||||| ||| | ||||||||||||||    |      |||   | ||  ||||  |    |  | || |   ||   ||| || | |    | ||| | |  | |   |||||     |||||
GGGGTGCTTCAATTTCTCTAACATACATTGCCTCAGAACGGATCATTCCTGGgtatacctc-tgctttcctgatttgctcaactggctta--tgattcttgcaacaaactattttaggggaatctta-acttttgaatttcac---atgcag

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|124990475|gb|EL062744.1|EL062744
EST:     GTGCTTCAATATCTCTTACTTACTATTGCCTCTGAAAGAATCATTCCTGG                         GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCA
genomic: GTGCTTCAATATCTCTTACTTAC-ATTGCCTCTGAAAGAATCATTCCTGGgtaaggatgg ... ttctgtgcagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCA
EST: gi|164045473|gb|ES102388.1|ES102388
EST:     TCTCTTACTTACATTGCATCTGAAAGAATCATTCCTGG                         GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACG
genomic: TCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatgg ... ttctgtgcagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACG
EST: gi|47829300|gb|CK118984.1|CK118984
EST:     GGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGG                         GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACG
genomic: GGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatgg ... ttctgtgcagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTGCTTCAATATCTCTTACTTACATTGCCTCTGAAAGAATCATTCCTGGgtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcag

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