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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGTTGATATTGGATCATCAACTGTTGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgatcttgttctttttctttcgttttaattagtaatcaggctaaaaaattggtgaaattatacatcaattatcttgtggaagagtctccgataatggcaatgccatttaccttccgaacaaatttgttattcttctatactagtgattctaaattttaatttctgtacatcattttgttcag

Basic information

species Glycine max
transcript GLYMA12G29750.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29750.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM2G069976_T01 (Zea mays), 5'ss of exon 21
TGGAGTTGATATTGGATCATCAACTGTTGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgatcttgttctttttctttcgttttaattagtaatcaggctaaaaaattggtgaaattatacatcaattatcttgtggaagagtctccgataatggcaatgccatttaccttccgaacaaatttgttattcttctatactagtgattctaaattttaatttctgtacatcattttgttcag
||||||||||||||| |||||||| || ||| ||||||| ||||| || || ||||| ||| | ||| |||| || || || ||||| || ||  ||||||||     ||| |||   |      |      ||    |  |||   | |||  |     | |||   |||  ||       || ||   || | ||  ||   ||  |                                                                               
TGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTACAGgtatc-caatcgtgtatctagctaattcacaaaacccctgttcata-tgaaatttcctcaagattgagcatacatc------tgtaaagatcacagaagatt-taagac-------------------------------------------------------------------------------

upper sequence: GLYMA12G29750.1 (Glycine max), 5'ss of exon 20
lower sequence: AT2G28320.1 (Arabidopsis thaliana), 5'ss of exon 20
TGGAGTTGATATTGGATCATCAACTGTTGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgatcttgttctttttctttcgttttaattagtaatcaggctaaaaaattggtgaaattatacatcaattatcttgtggaagagtctccgataatggcaatgccatttaccttccgaacaaatttgttattcttctatactagtgattctaaattttaatttctgtacatcattttgttcag
 || ||||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||||||| | || || || || ||||| || |||||||||||||| | ||  |     | ||   | |||| |||    | |||   |       |  |    ||| | ||  |              ||  |  |||    |  | || ||||    |  |  ||                                                              
GGGCGTTGATATTGGGTCATCAACTGTTGCAAGAGGAGTTGTGAGTCTTGTTCTTGGTTACCTCAACAAACTCGTGATTGAAATGGCCTTCTTAATACAGgtaaactaat--taccaatctttcctggtttaaatcta-agtcaacttcggtgggtattctggttacatattga--------------agcattggatttgagtga-gcaatttcttctttgtgcag-------------------------------------------------------------
















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|209712559|gb|BW653715.1|BW653715
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|7326871|gb|AW620669.1|AW620669
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|22933067|gb|BU550206.1|BU550206
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|20448896|gb|BQ253020.1|BQ253020
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|192327435|gb|FK018167.1|FK018167
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|209705116|gb|BW653339.1|BW653339
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|209722676|gb|BW654683.1|BW654683
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|19053571|gb|BM732238.1|BM732238
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
EST: gi|213610817|gb|DB975070.1|DB975070
EST:     TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAG                         GGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT
genomic: TCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgat ... ttttgttcagGGAAACACACGTGAAGAGCTCCCTGAATTTCTTCTTGGAACTTGCCGCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGTTGATATTGGATCATCAACTGTTGCAAGAGGTGTTGTGAGTCTTGTCCTTGGGTACCTCAACCATCTGGTTATAGAGATGGCATTTTTAATACAGgtaaagtgatcttgttctttttctttcgttttaattagtaatcaggctaaaaaattggtgaaattatacatcaattatcttgtggaagagtctccgataatggcaatgccatttaccttccgaacaaatttgttattcttctatactagtgattctaaattttaatttctgtacatcattttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG