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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA

Basic information

species Glycine max
transcript GLYMA13G39990.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 6
--gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgttctgt------agTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
  |||  ||  ||||   || ||  | | |||   || ||||  | |   |||||   ||  |  |||    |||||  | | |   ||| |||||       ||||||||||| ||||||| ||  || | ||||| ||||||||||||   |||||||||||| ||||||||||||||| | | || || ||||| || | | 
atgtttgtgtcattggacactttactttgtat---ttaatttaaacac--accatgaaattgtaacttgtcaattgcctaatcttttatttttctgctgttgcagTTTTCTGATAATTTTGCTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTAC

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gttattgatattgact--acctt-catatatatgaatt--tatttgtatatctaccatttcatattttcttcaagattgctga--ctatcaaa--ttgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                                                          || |  ||||   | |  | ||| |||     |||| |  || |    | |     || | |   |    | |    | ||||    ||  ||  || |  | |||||||| ||| | ||  | ||  |||| || ||||||||||| ||||||| |||||||||| ||||||||||||| |  || || |||||||| || |  |
gtaactgagacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggtgaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACTGAATGGGATGAATTTGAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------gttattgatattgact-accttcatatatatga-atttatt-tgtatatcta-ccatttcatattttcttcaag-attgctgactatcaaa--ttgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                                                                                  |     | |   ||| |  ||||  |||| |  || |||  ||  ||   |   |  | | |  |   |||   | | |  | |  ||    || || | |||||||| ||  | ||  ||||| || | || || |||||||||||||||| ||| |||||| |||||||||||||||  || || || ||||| || |  |
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcatctatcatgcttaaacagttaactgagacatctatcattcacttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttc-ttcaagattgctgac----tatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                                                           |  | |||| |  ||||  |    ||   ||| |  | |||||        |||| | ||   | | ||    | |  |     | |    || || | |||||||| ||  | ||  | ||| |||| || ||||||||||||||||||| ||| |||||| ||||||||||||| |  || ||||||||||| || |  |
gtaactggcagactgccatcttacctgcttaaccttggtgcaccaaacttctgagctttgggactgatgtacactagatctgcat-cgtgattaaacttgtagtcactttatttgaaatgagcatgcagtcctaccaatttcatgtatgtttcttttatagTTTTCAGACAAATTCACTATTATGCTGTTCCATTATGATGGTCGGACTACTGAGTGGGATGAATTTGAGTGGTCTAAAAGAGCAATCCATGTGAGTGTCA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 6
gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaat---tgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                    | | | ||   || |  ||   ||||        | |||| || |  |   || | || |  || ||   |  |||  ||||||| ||| | ||  ||||| || | || ||||||||||||||||| | ||| |||||| |||||||||||||||  || ||  ||||||| || |  |
-------------------gtaagacatcctaaatgcttaaaatatgcgaggaatgatatattgt--agtttttcagattcacatatgtcttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatat-----tttcttcaagattgctgact----atcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                                                           |  | |||| |  | ||  | || ||   ||| |  | |||||        |||| | ||     | |  ||     | |  | |     | |  || || | |||||||| ||  | ||  | ||| || | || |||||||||||||||||||  || |||||| ||||||||||||| |  || ||||||||||| || || |
gtaactgacagactggcaccttacctacttaagctcagtgtatcaaacttctgaactctgggactgatgtacagtagatccacat-cgtgattaaacttgtagtcactttatttgaaatgagcatgtagtcctttcttccaatttcacgtaagtttcttttatagTTTTCAGACAAATTCACCATTATGTTGTTCCATTATGATGGTCGGACTACAGAGTGGGATGAATTTGAGTGGTCTAAAAGAGCAATCCATGTGAGTGCCA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 6
gttat-tgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgt-tctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
||| |   ||||   | |  |   |    | | |||  ||| |||||       ||  |   | |    |||||  |   | ||   |  | |||  |||||||||| |||||   |||||||||||| ||||||||||| ||||| | ||||||||| |||||||||||||| | ||| || || ||| | ||  |||
gttctgcaatatcagc-atgtgttttagcaagtattgttttatatattc-----tttgtggatacactcagattttttgttttcttgtcatatcttcagTTTTCTGAAGATTTCCAAATTTTGCTCTTCCATTATGATGGCCGGACAACTGAATGGGACCAATTTGAGTGGTCGAAGAGCGCGATTCATATTAGTACAA

upper sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
|| ||  | ||   |    | |||| || |  ||||||||  || |  |   ||||    | |        || | ||   | |  || |   | |||||||||| |||||   ||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||  | |||||| ||||| || ||||
gtcatccacatgagccgt-tccata-attttcatttattt--attttgattgtttctggatatt----gagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA

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|33390489|gb|CA853684.1|CA853684
EST:     TCACTGTTGGTTATGAACAGAGGCATAATATCAATGCTGCAGTGAAAAAG                         TTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGT
genomic: TCACTGTTGGTTATGAACAGAGGCATAATATCAATGCTGCAGTGAAAAAGgttattgata ... tgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGT
EST: gi|13181457|gb|BG352797.1|BG352797
EST:     GTTGGTTATGAACAGAGGCATAATATCATTGCTGCAGTGAAAAAG                         TTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGT
genomic: GTTGGTTATGAACAGAGGCATAATATCAATGCTGCAGTGAAAAAGgttattgata ... tgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatctaccatttcatattttcttcaagattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA
                              tgctgac  putative branch site (score: 2)
                                            ttgttct  putative PPT
         atttcatattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG