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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcatatagactatagagtataaacacacgtatatccacgccatcagtgggttacttgaggtatatggtaatcatttgatgtatgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC

Basic information

species Glycine max
transcript GLYMA16G28310.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
-----------aattcatatagacta------tagagtataaacacacgt-atatccacgccatcagtgggttact--tgag-gtatatggtaatcatttg----atgtatgatt--ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
           ||||  | | |||||      ||    | ||  |   || |||    || | |     |   |||  |||| |   |   || |||| ||     | |||| ||  |||||||||||| ||||||||||| || |||||||||||||||||||| ||||| ||||| |||||    ||||| || | 
gtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 5
-----------------------aattcatatagactatagagtataaacacacgtatatccacgccat----cagtgggttacttgaggtatatggtaatca--tttgatgtatgattc--------tctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
                       | ||| | |      | |   ||  | || | |   |   | | ||    ||    | ||||    |  | |||  ||||  |||  ||  || |||          ||||||||| |||| |||||| || || |||||||| || ||||| || ||||||||||||||| | ||||| || | 
gttaatgataaaaaaaactccacacttcttttctttcctggctgatcgatacccctg-gttagcactataaaacaaaatggtactacttgagtttgggtatcacgttttgtgcgtgcttcgttcttttcttgtgcagATACCAAGGAAAGGGAAGATCTATTCAGTCAACGAAGGGAACGCCAAAAACTGGGATGGGCCTACAGCCAA

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 7
aattcatatagactatagagtataaacacacgtatatccacgcca---tcagtgggttacttgaggtatatggtaatcatttga---tgta-tgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
        | || ||| |     | |  ||| | | |       |   |||      ||| |||  | | | ||   | || ||   |||  ||  |  |||  ||||| ||||||||||| |||||||| ||||| |||||||||||  | || || ||||||  ||| || || | 
-------gttgagtattggcctaacaagcacctttgttggtttaaatttcatctttgtacatgatatctctagtttactttggagcttgtgctgccttcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAATTGGGATGCTCCAACAGCCAA

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S1_300V6.2 (Physcomitrella patens), 3'ss of exon 7
------aattcatatagactatagagtataaacacacgtatatccacgccatcagtgggttacttgaggtatatggtaatcatttgatgtatgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC-----------------------------
        ||  |   || |      | ||||  |  ||      | | | |   |   | | |||    |  || |||||   |  | | |  ||   |   ||||| || || || || || ||||| || ||||||||||||||||||||| |||||||  | || ||  | |                              
acacttggtttttgatgatttgttcttgtaaagtccagttggcttatgacct---tccatcatttg---caactgttaatctgatcgtttctatttgcttcgtcagATTCCCAAAAAGGGCAAGATTTACTCTGTGAATGAAGGAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ04554 (Selaginella moellendorffii), 3'ss of exon 7
aattcatatagactatagagtataaacacacgtatatccacgccat--cagtgggttact-tgaggtatatggtaatcatttgatgtatgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
               ||   |   || | | |  |     |   ||  || ||| | | | |||| |       |     ||||||  |  || ||| ||||||| |||||||| || ||||||||||| |||||||| || ||||| || ||||||||    || |||     
--------------gtaagttcgtaaaagatgattcctttcattattacaatggatgattgtgagatgcccaaga-----ttgatgatt--ttttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ36627 (Selaginella moellendorffii), 3'ss of exon 6
aattcatatagactatagagtataaacacacgtatatccacgccatcagtgggt-tacttgaggtatatggtaatcatttgatgtatgatt--ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
                      |||   |   ||     |  || |   |   |  | | || |  | ||  |  |    |||  ||||||   ||| ||||||| |||||||| || ||||||||||| |||||||| || ||||| || ||||||||    || |||     
---------------------gtaagttcgtataagatgattcctttcattattacaatggatgattgtgagatgcccaagatcgatgattgcttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

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|31474714|gb|CD416742.1|CD416742
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|26269057|gb|CA820120.1|CA820120
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|31457542|gb|CD399570.1|CD399570
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|6070043|gb|AW099600.1|AW099600
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCCAAGAAAGGTATAATCTATTCAGTGAATGAATGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|31469604|gb|CD411632.1|CD411632
EST:     GTTCATCCTTACTCACCCTTACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: GTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|151398810|gb|EV268681.1|EV268681
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
EST: gi|192304054|gb|FG993884.1|FG993884
EST:     CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG                         ATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC
genomic: CCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgtattgctct ... ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtgggttacttgaggtatatggtaatcatttgatgtatgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC
                              atttgat  putative branch site (score: 5)
                                           ttctctgt  putative PPT
                         taatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcatatagactatagagtataaacacacgtatatccacgccatcagtgggttacttgaggtatatggtaatcatttgatgtatgattctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - aacacac
- - - - - - - - - - - - - - - - - - -ccacgcc
- - - - - - - - - - - - - - - - - - - - - - - - gtgggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatga