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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaataattgatgttctgttactgatatatatgaatatgaatcactgtacacatcgagcttgttatctggttgcatttgctgagagttgttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCCAACTTTTGCTGAAAGGATAGTGATCAACCATAGAGAGTACTTCAAAAAG

Basic information

species Glycine max
transcript GLYMA12G09940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09940.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g00680.t01 (Vitis vinifera), 3'ss of exon 1
agaaataattgatgttctgttactgatatatatgaatatgaatcactgtacacatcgagcttgttatct--ggttgcatttgctgagagttgttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCCAACTTTTGCTGAAAGGATAGTGATCAACCATAGAGAGTACTTCAAAAAG
  || | | | ||  |   ||| |    || |  |   |   |    | | | | |    || ||||||  |||   |  | |  |       ||||  |||||| ||||| |||||||| ||||||||||| ||||||| | |||| || ||  | ||||| || ||   ||| |||||||| ||||| ||  |||  || 
-aaattgaataataattcattaattcattaaacaagc-tagctagaagaatatacctttgttattatcttgggtgctaagtccaaaataaaactgaaatcagGAAGGAATACTTTGAGATCCCATGGGCAAGCTTGAGGGCAATGGTGGAACCGTCATTTGCAGAGAGATCAGTCATCAACCACAGAGATTATCTCACTAAT
















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|4396359|gb|AI495356.1|AI495356
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|213611740|gb|DB958862.1|DB958862
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|192333062|gb|FK024711.1|FK024711
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|8284144|gb|BE021703.1|BE021703
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAGGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|254331043|gb|GR842308.1|GR842308
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|38193050|gb|CF922256.1|CF922256
EST:     AACCTTGCAAAAACTATGCAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|254328690|gb|GR833062.1|GR833062
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
EST: gi|254329113|gb|GR833485.1|GR833485
EST:     AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCC                         GAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC
genomic: AACCTTGCAAAAACTATACAACATCAAGCCAACGTCACCCTTATTGATCCgtgagttctc ... ttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtacacatcgagcttgttatctggttgcatttgctgagagttgttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCCAACTTTTGCTGAAAGGATAGTGATCAACCATAGAGAGTACTTCAAAAAG
               ttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaataattgatgttctgttactgatatatatgaatatgaatcactgtacacatcgagcttgttatctggttgcatttgctgagagttgttgaacacagGAAAGAATATTTTGAGATTCCATGGGCAAGTTTGAGGGGATTGGTTGAGCCAACTTTTGCTGAAAGGATAGTGATCAACCATAGAGAGTACTTCAAAAAG

agaaataa
- - - - -tgatgtt
- - - - - - - - - gttactg
- - - - - - - - - - - - - - - - - - - - - -cactgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt