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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgtgttctaactctcaacccctttccttctgaacttacaatttttagtataaaattcatttcataccctcttaaatatatgttattgtatata...

Basic information

species Glycine max
transcript GLYMA06G42840.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 5'ss of exon 2
GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgtgttctaactctcaacccctttccttctgaacttacaatttttagtataaaattcatttca-taccctcttaaatatatgttattgtatata-
|| ||||| ||  |||| |||||||| ||||| || |||||||| || || || ||||| || |||||||||||||| || ||||| || ||||| |||   |  | |    |  || | |||   |    ||||   | ||   | |      |  |   || |||| | |  ||  | |  |   |  | |  
GAAATGTCTGCAGCTGTTATTGAGGGAAATGACGCTGTTACTGGTCATATCATTTCCACTACTATTGGAGGCAAAAACGGCGAACCAAAGCAGgtttgatgctaatgtt-tgcaaaatctcttagataactaactagtagttaacacttacggttatagcacagtaccatgtgtaaggttt-ctgcggggtctgg

upper sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 2
GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgtgttctaactctcaacccctttccttctgaacttacaatttttagtataaaattc-atttcataccctcttaaatatatgttattgtatata
|| ||||| ||| |||| || || || |||||||| ||||| || |||||||| || || |||||||||||||||||||| ||||||||||||||  || | |||| |   |   | |    |      | || | | | || ||  |  |  |  | |     ||     |||  || | |||    |  || 
GAAATGTCTGCTGCTGTTATAGAAGGAAATGATGCTGTTACCGGTCACATAATTTCTACTACAATTGGAGGCAAAAATGGTGAACCTAAACAGgttggattctgttgtttattaaatctttgtaatgatttaaatcatagttattgctcgagcacactaccatgtataaggttaccta-aggtttggattaatc

upper sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 2
GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgtgttctaactctcaacccctttccttctgaacttacaatttttagtataaaattcatttcataccctcttaaatatatgttattgtatata---------
|| ||||||||| |||| ||||||||||||||| | || ||||| || ||||| |||||||| ||||||||||||||||| || |||||||||||| || |  | |||   |  | |  |||    | |   | |||    ||||   || |      |||  |  |||  || | |||||  |||| ||  |         
GAAATGTCAGCTGCTGTTATTGAGGGGAATGATCCAGTCACTGGTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttggatct---ttcctattcctcgaatgc--gagttattccttttgacatta---ctgttttttttccttctata-atatgcaattgcattcaagggtttaa

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|120530050|gb|EH258184.1|EH258184
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|37996099|gb|CF807688.1|CF807688
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|193416669|gb|FK384125.1|FK384125
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|120531619|gb|EH259752.1|EH259752
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|5058337|gb|AI736813.1|AI736813
EST:     CACATAATCTCCACCACAATTGGAGGCCAAAAGTGGG-AACCCTAAACAG                         ACCATCAGTTACATGGCACAACGTGATGATGGCACTGGATCATTTGGAGT
genomic: CACATAATCTCCACCACAATTGGAGGCAAAAA-TGGGGAACC-TAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGT
EST: gi|208268482|gb|GE069393.1|GE069393
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|193433005|gb|FK395713.1|FK395713
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
EST: gi|42723166|gb|CK769065.1|CK769065
EST:     GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAG                         ACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT
genomic: GCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgt ... ccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATGTCAGCTACTGTCATTGAGGGGAATGATGCCGTTACTGGCCACATAATCTCCACCACAATTGGAGGCAAAAATGGGGAACCTAAACAGgtgtgaatgtgttctaactctcaacccctttccttctgaacttacaatttttagtataaaattcatttcataccctcttaaatatatgttattgtatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctt