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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT

Basic information

species Glycine max
transcript GLYMA18G06770.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtga---gatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
     ||| |        |  || ||      |     ||  | ||  |        | || |        |    | | |||    |  | |    ||||| | || |||||||| || ||||||||||| ||||| ||  | ||||| |||||||||||||| ||||| |||||| | | |||| |  | |  ||   | |
-----gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACTCCACAGCAGGGATTT

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 21
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
                 |||    |       |   |  || ||  |||   |    || ||||     | ||  | | ||||   || |||| |  || | || || || || || || |||||||| ||||| |||||||||||  ||||||| || || ||||| |||||||||| |||||  |  |||    ||  
-----------------gtgatgatacatttgactttc-ctcttcttgatcaaatgcga-tatgtctgagctaa-tgatgtgattgttctcatgt--agATGCCACTACACACCATAATCGAGATACAAATGGGCGTCACGGGTGTGGAAGAGAAGAGGTACAAACTCATGGACTGAA-TGAATACATAAAAGCAGCTGG

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 22
---------cttttgtggggttc---atcgtgtcagttggag-aaatcatga-cttttgatgaatgatgatgaatatgctgaggatatc-taacgtgagatttgtcatttc--caggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
            ||      | |   |   | | ||   ||   |   || | ||||    || |  ||      | ||     | ||  |||| | |  || |   ||||  ||| | || ||||| || || || |||||||||||||||||  | ||||| ||||||||| | || ||||| |||||||||| | ||   |  |  |   |   
gtaaaatctgaattagaaaatacgagactatcttagaacgattgagctataagctttcagagagtcttggctg-caagccacacacataataacat-attttggatgtttcaacagATGCCACTTCACACTATAATAGAGATACAGATGGGAGTTTCTGGTGTGCAAGAGAAACGCTACAAACTCATGGACTGAATTCAAACAACTATTACCACAA-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
---------cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatga-atatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
         | |||   |  |  ||    |   | ||||||   |  ||  |  |    ||   | |  | |  ||||  | |  ||| |    |||     ||| ||||| || |||||||| || || |||||||| |||||||| || |||||||||||||||||||| || || |||||||||  |   || |   ||  || |  
ttaccacatcattttatgaataaattccttttctaggagaag--aaaacaatccaaagttggccaagttacaccctgacaa-acttaatg----attcac--ttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGCTTCACAGAATCTTTTG-

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: EFJ11749 (Selaginella moellendorffii), 3'ss of exon 17
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
                   || |||  | | |||        |  ||      ||   ||  | ||      | ||   |     |||||   | |||| | |||||||| || || |||||||| |||||||||||| | ||||| ||||||||  |||| || ||  |  |                           
-------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCGCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA--------------------------

upper sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
lower sequence: EFJ22544 (Selaginella moellendorffii), 3'ss of exon 17
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
                   || |||  | | |||        |  ||      ||   ||  | ||      | ||   |     |||||   | |||| | |||||||| || || |||||||| |||||||||||| | ||||| ||||||||  |||| || ||  |  |                           
-------------------gtgagtgagtggaatttatctagtcaatatgatctggccaagttccttctttaagcttctgcttcctttgtg--tgccagATGCCTCTTCACACTATCATTGAGATCCAGATGGGAGTCCCAGGTGTACAAGAGAAGCGATACAAGCTCTTATAA--------------------------

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|8669465|gb|BE190572.1|BE190572
EST:     ATATGCTTATTTTGCTGACAAGCCTTTGAACGAAATTTCGCATATAGAGG                         TTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGT
genomic: ATATGCTTATTTTGCTGACAGGCCTTTGAACGAAATTCCGCATATAGAGGtaatttgtga ... catttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGT
EST: gi|31473640|gb|CD415668.1|CD415668
EST:     CGAAATTCCGCATATAGAGG                         TTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAG
genomic: CGAAATTCCGCATATAGAGGtaatttgtga ... catttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAG
EST: gi|31305977|gb|CD391180.1|CD391180
EST:     ATATGCTTATTTTGCTGACAGGCCTTTGAACGAAATTCCGCATATAGAGG                         TTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAG
genomic: ATATGCTTATTTTGCTGACAGGCCTTTGAACGAAATTCCGCATATAGAGGtaatttgtga ... catttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT
                           atctaac  putative branch site (score: 2)
                                            tcatttcc  putative PPT
          atgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtgagatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- -ttgtggg
- - - - - - - - - - - -gttggag
- - - - - - - - - - - - - - - - -tcatgac
- - - - - - - - - - - - - - - - - - - - - - - - - -gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgagg