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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA

Basic information

species Glycine max
transcript GLYMA07G39380.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtttaacctggattaaaattcttttgacca-tacatttgctaatggcatctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                                                                                            |  |  |||||      |   |||||   | | || ||  | |   ||   | ||     || |          || | ||||  |||||   || ||||| || ||||| ||||| ||| | || ||||||||||||||||  || ||||||||||| || ||||||||||  ||||| || |||||||||||||| |||
gtaagcgttttttttttaattttgtgaactgagcaataacttggttggtagacttcccactgaggaggccacccctgagaattagtttcagggagttccctggccagctagggttttgggtactccacttttttaatacaaagccatgaaatgtcatctccaactctctcatgtag-cttttgttat-tgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGTGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 11
gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctctatctttggttagaatttgtag---tcacctgta-ctcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
      |  ||| |   ||     ||        ||| ||| |    |  |  |      ||    |||  |    || | || | ||  |||   || ||||| || ||||| ||||| ||| | || ||||||||||||||||  || ||||||||||| || ||||| ||||  ||||| || |||||||||||||| |||
----gccagggaatgtcatctccctgtggtggttttttctattaattttgcgtttccaaatttttctttccaactctctcatgcagcttctttgctatttgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
------------gtttaacctg--gattaa--aattcttttgaccatacatttgctaatggcatctctatctttggttagaatttg--tagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
             |||   ||     ||||  || || ||  |  |||||||   || |   ||   | |   |  |   |  |||  |  |    |||| ||   |  ||||  ||| |||||||| ||||| |||||||| || ||||||||| | || ||||| |||||| | |||||||| |||| ||  |||||  | ||||||||||| |||
gtaagttacgcaatttgttctttcagttaaccaaatcgttatataatacattgcttatt--tattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaata--cagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 11
gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctct--atctttggttagaatttgtagtcacctgtactcttttaaaatatgc---agCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                             ||  ||| ||  |   ||| | |  ||   |  ||||  |    |    | | | ||| ||   | | ||    || |||||||| ||||| ||||| || || ||||| ||| | ||||||||||| ||||| ||||| ||||||| | | || || || || || ||||| |||
--------------------------gtaatgaattagcctaaaacatttgttaataactaattagcgtcaacataatcatattctcattctcattgtgttttagGTATGAAGGAAGATGCGGCTTACCTACAAATTTCGATGCAACTTACTGCTACGCATTAGGTTACGGTGCTGGATCACTTCTCCAGAGCGGAAAGACCGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------gtttaacctggattaaaattcttttgaccatacatttg---ctaatggcatctctatct---ttggttagaat-ttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                                                         |  ||        |  ||  | ||   || |   |||   |||    ||   | || |   || ||||  |   | |  |    |     | |     || ||||| ||||||||||| ||||| || |||||||| || ||| || | ||||||||||||||||||| || ||||| ||| ||||||||  ||||||| ||||| 
gtatgtaccatcttttgatgaaaaaggatatagctattttgagtcacatatttcaattacaagtaatgacatgatattcttactcaaattgttgaacctacccccacaacaatttatgttagttatgacactatgttttgtttctggcatccctgatgtgcagATATGAAGGGAGGTGTGGTTTTCCAACTAACTTCGATGCTGCCTACTGCTATGCATTGGGTTTTGCTGCTGGAGCTCTCCTTCACTGTGGGAAAACTGGG

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 11
gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                                           |  || | | |     |     | |||| |  |||   |  ||   |   | |  || ||||||||  | |||||  | || || ||||||||||| |||||||||||||| ||||| ||||  || | ||| ||||||||   |||  |||| |||
-------------------------------------------gtaatgttttttcccagc--acagttgttgctacc---atgctaacaggctgtatagATATGAAGGCCGGTGTGGTCTACCGACAAATTTTGATTCAACTTACTGCTATGCGTTGGGCTATGCCGCAGGAGCGCTCCTTCATGCTGGACAGACAGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 11
gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                                                   | | |||    || |   || ||  |   ||  ||   |   | |  || ||||||||  | |||||  | || || ||||||||||| |||||||||||||| ||||| ||||  || | ||| ||||||||   |||  |||| |||
-----------------------------------------------gtaatgttttttcccagcaca-gttgttgctactatgctaacaggctgtatagATATGAAGGCCGGTGTGGTCTACCGACAAATTTTGATTCAACTTACTGCTATGCGTTGGGCTATGCCGCAGGAGCGCTCCTTCATGCTGGACAGACAGGA

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|26058870|gb|CA801784.1|CA801784
EST:     CAACAGGGCACATATAAAGGAGGATTTAGGGGGCAGTCCCACTTTTTCGG                         CTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTA
genomic: CAACAGGGCACATATAAAGGAGGATTTAGGGGGCAGTCCCACTTTTTCGGgtactccgtc ... aaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTA
EST: gi|298181953|gb|HO026128.1|HO026128
EST:     CAACAGGGCACATATAAAGGAGGATTTAGGGGGCAGTCCCACTTTTTCGG                         CTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTA
genomic: CAACAGGGCACATATAAAGGAGGATTTAGGGGGCAGTCCCACTTTTTCGGgtactccgtc ... aaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA
                                   tactcttttaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaacctggattaaaattcttttgaccatacatttgctaatggcatctctatctttggttagaatttgtagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - -gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctgt