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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttctgctagtaagttttaacatcctctgattacattgtctttattgaagaaacccctttttgtttgtcttctaaaaaaactgttaaaatatgt...

Basic information

species Glycine max
transcript GLYMA15G05490.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G25280.3 (Arabidopsis thaliana), 5'ss of exon 3
CTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttctgc--------tagtaagttttaac------atcctctgattacattgtctttattgaagaaacccctttttgtttgtcttctaaaaaaactgttaaaatatgt---------------
| ||||| || ||  | ||||| |||   || |||||| |||| |||||||||||||| |||||||| ||||| || ||| ||||| | |||||||| ||||  |||||| |         |||||  ||   ||      ||  | || |    |     || || ||  || |  || |  ||    ||  |  ||   |  | |  | | |               
CAGCTAAAAGAACTCGTAGAACTACTCGAACCGAGTACATTATCTCCATGGATGCTGATAACATCTCAAGATCCAGCAACTCTTACCTCGGAAAGCTCAGgttcgttttcagtcctagacatagtagtttgctactgttgaatattatggtcgtttatctattgttcaaataatcttttgtgattcccatttaatcaagcttaatgaggtttctttatctctctctcag

upper sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G43640.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttctgctagtaagttttaacatcctctgattacattgtct---ttattgaagaaacccctttt-tgtttgtcttctaaaaaaactgttaaaatatgt
| || ||| |  || ||||| | || ||||| ||||| || || || |||||||| |||||||| || |||||||| | |||||||||||| || |||| || ||        |   ||     |||||| |  |   ||||  | |   || ||||  ||  |        |||||||||   |    | | | |        
CGGCAAAGCGCTCACGGAGAGCTACATACACAGAGTATGTAATATCAATGGATGCAGACAACATTTCAAGATCAAGCAGCACTTACATTGGCAAACTGAAgtaagaagaagatttaaaaaa---aacatcattcgtccacatgttttgagttcttgattaattcagacaaacgtttgtctt---acttcattttcag-------

upper sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv12s0055g00460.t01 (Vitis vinifera), 5'ss of exon 5
CTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttctgctagtaagtttta-acatcctctgattacattgtctt-tattgaagaaacccctttttgtt-tgtcttctaaaaaaactgttaaaatatgt
|||| || ||||   |  | ||||||| ||| ||||| ||||| |||||||||||||| ||||| || || ||||| | ||||||||||||||| ||||||| |      |    |  |   | | | |||||    || |  | | || ||||| |   |||  | |  | |   |  || |    |  | |   ||||   
CTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTCAAGGTCAAGCAGCACTTACATTGGAAAACTGAGgtaatacaattatatgcgaacataacaaatccttgacttcctctctgttatattgtatttacctttatcgggtacatggtccatggcacttctaggaata---

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|208058706|gb|GD858178.1|GD858178
EST:     ATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: ATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|207708265|gb|GD692061.1|GD692061
EST:     AAGTAAACACTTACATTAGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: AAGT-AACACTTACATT-GGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|254325987|gb|GR838868.1|GR838868
EST:     GATGCTGACA-CATCTCTAGATCAAGTA-CACTTACATTGGAAAGCTGAG                         ATCAA-TTTTCTTGG
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGG
EST: gi|208319163|gb|GE113324.1|GE113324
EST:     TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|208335392|gb|GE133365.1|GE133365
EST:     GTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|208096689|gb|GD892914.1|GD892914
EST:     GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTAAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|9440416|gb|BE440921.1|BE440921
EST:     GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|193403081|gb|FK369027.1|FK369027
EST:     GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|6912855|gb|AW394339.1|AW394339
EST:     GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|207819081|gb|GD793215.1|GD793215
EST:     ATCAAGTAAACAACTTAACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: ATCAAGT-AAC-ACTT-ACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|193683959|gb|FK621445.1|FK621445
EST:     TCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGG
genomic: TCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGG
EST: gi|208206002|gb|GE002003.1|GE002003
EST:     TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|208204875|gb|GE005776.1|GE005776
EST:     TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: TGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
EST: gi|208323663|gb|GE122234.1|GE122234
EST:     GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAG                         ATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA
genomic: GATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttc ... catacaccagATCAAATTTTCTTGGTACAAAGTTCATTATATACGATACACAGCCTCCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTCTAGATCAAGTAACACTTACATTGGAAAGCTGAGgtgagttttctgctagtaagttttaacatcctctgattacattgtctttattgaagaaacccctttttgtttgtcttctaaaaaaactgttaaaatatgt

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaaa