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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttgcaattattttatatatgaatttgagctctcaattaacatagatgcttcacttgattacacaaaatgctgattgtaatataatgtatgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAG

Basic information

species Glycine max
transcript GLYMA11G14960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G28800.4 (Arabidopsis thaliana), 3'ss of exon 2
-----aacttgcaattattttatatatgaatttgagctctcaattaacatagatgcttcacttgattacacaaaatgct--gattgtaatataatgtatgaatac---agGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAG
         ||  |||| || |  | || |  |   ||    | |   ||  |   ||  | || |     | |||  |       |  | |  | |  |||| |   |||||||||| |||||||| ||||||||||||||||| ||||| || || |||||| |  | || || || ||||||
gttagtgagtgtgattagttgaattttgcagctcctcttgtcactttgattcaattttggcatgttggttgagaatttttgagcattgcttttgttttggaatcctttagGTTGAATCAACACTAGCGATGCAAAATCTTCAACCGAAAATCAAAGCGATTCAACAACGTTACGCAGGAAATCAG

upper sequence: GLYMA11G14960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 2
---aacttgcaattattttatatatgaatttgagctctcaattaacatagatgcttcacttgattacacaaaatgctgattgtaatataatgtatgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAG
   ||  ||   | || |     ||     ||   | |  | |      ||||   |  ||| |      | ||| |||   |  | |  | | || ||  |||||||||| ||||| || |||||||||||||||||||| || |||||||||||||| ||||||   |||||||||
agcaagatgtt-tcatgtccatcattcccatgtaatattgacttctgctgatgacactgttggtgctgttatatgatgacatt--tgttgtatttgtatgtagGTTGAATCAACACTGGCCATGCAAAATCTTCAACCAAAGATCAAGGCCATTCAAGAAAGATATAAGGGCAATCAG
















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|10846772|gb|BF071420.1|BF071420
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|14258971|gb|BG881879.1|BG881879
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|10235360|gb|BE804248.1|BE804248
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCGAAATCTTCAACCATAGATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|10235184|gb|BE804072.1|BE804072
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCAAAATCTTGCACCCAAAA-TTAAGGCCAT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTT-CAACCAAAAATTAAGGCCAT
EST: gi|19347107|gb|BM891987.1|BM891987
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
EST: gi|209708316|gb|BW683906.1|BW683906
EST:     TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAG                         GTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT
genomic: TGCTCACTGTTATAGTTAAGGCCGCTACGCTTCCCTTGACAAAGCAACAGgttggtacaa ... atgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgcttcacttgattacacaaaatgctgattgtaatataatgtatgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAG
                         tgctgat  putative branch site (score: 3)
                              attgtaatataatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttgcaattattttatatatgaatttgagctctcaattaacatagatgcttcacttgattacacaaaatgctgattgtaatataatgtatgaatacagGTTGAATCTACACTAGCTATGCAAAATCTTCAACCAAAAATTAAGGCCATTCAAGATAGATATGCTGGCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat