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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagttctatatttaatgctccatccttcatggtatagaatcttatattttatttgagacaacttcttgaagtcctcaatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG

Basic information

species Glycine max
transcript GLYMA07G18470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G19340.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 4
---------aaagt-tctatattta-atgctccatccttcatggtatagaatcttatattttatttgagacaacttcttgaagtcctcaatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG
         | |||  || || |||    |    | | || |||| || || | || |||| |||      |  | |||  |||  | | ||||   |    |    ||||||||||| || ||||   |||| |||||||| ||||| ||||| |||||||| ||||| || ||||  || |||||||| ||||||
tcattgctgacagtacctgtacttatgaacagtgttcctcctggtgtacaaccataaattt-att------atttgcttatagt--ttattctaacct--cttgtattcagGAAATTTCCACTGGACAGTTGAAGATGTTGCAAAATCTATTGTCTGCATGATAATGTCTGGTCCATGTCTTACAGGATACACACAG

upper sequence: GLYMA16G19340.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 4
--aaagttctatatttaatgctccatccttcatggtatagaatcttatattttatttgagacaacttcttgaagtcctcaatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG
  | ||| |  | |  |    |   | |||      || |   |||    | |   |   |    |  || | ||  |    |    ||      |  ||||||||||| || ||||   |||| ||||| || ||||| ||||| |||||||| ||||| || |||| ||| |||||||| ||||||
acagagtacagtgtccagctgtt-gtgcttatgaacattgctccttggcatatggctagtatgtatgatt-atgttgttttcccctcatctgtctcattcagGAAATTTCCACTGGACAGTTGAAGATGTCGCAAAATCTATTGTATGCATGATAATGTCTGGTCCATGCCTTACAGGATACACACAG

upper sequence: GLYMA16G19340.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 4
aaagttctatatttaatgctccatccttcatggtatagaatcttatattttatttgagacaactt---cttgaagtcctc---aatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG
         || || ||| ||| |     ||  |          |  |||  | | ||    |||   ||| || | ||    |    | | || || |  || ||| || || || |||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||  || || || |||||||||
------gcttaattgatggtccctggcaaatttttgccggaacaaggtttcttctaagctctcttgcccttaaattgcttctgaccagattttgctcacatgttagGGAACTTCCACTGGAATTTGGAGGATGTTGCCAAATCAATTGTTTGCATGATTATGTCTGGCCCATGTCTCACTGGCTATACACAG

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|16282058|gb|BI944813.1|BI944813
EST:     CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG                         GAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
genomic: CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaatt ... ctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
EST: gi|192328987|gb|FK021398.1|FK021398
EST:     CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG                         GAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
genomic: CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaatt ... ctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
EST: gi|213593823|gb|DB957943.1|DB957943
EST:     CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG                         GAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
genomic: CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaatt ... ctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
EST: gi|213619704|gb|DB967326.1|DB967326
EST:     CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG                         GAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
genomic: CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaatt ... ctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
EST: gi|24205788|gb|BU965041.1|BU965041
EST:     CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGG                         GAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA
genomic: CACTTGGCCTCCGTTAGTTTGGGGTGTAGTTTGTGGTGCTGCTGCCTCGGgtactaaatt ... ctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttatttgagacaacttcttgaagtcctcaatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG
                                            tctcc  CT-rich tract
     tatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagttctatatttaatgctccatccttcatggtatagaatcttatattttatttgagacaacttcttgaagtcctcaatctactatgatctccggtcagGAAATTTTCATTGGAATTTTGAGGATGTTGCTAAATCAATTGTGTGCATGATGATGTCCGGCCCATTCCTGACAGGATATACACAG

- - - - - - ttaatgc
- - - - - - - - - -tccatcc
- - - - - - - - - - - - - ttcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacttc