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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatactgagattcacatatcagcaaaagaatctggattctgagctgcatttctgtattggaccactttatagtttatatgacacatccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG

Basic information

species Glycine max
transcript GLYMA08G20930.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g37760.2 (Oryza sativa), 3'ss of exon 3
aatatactgagattcacatatcagcaaaagaatctggattctgagctgcatttctgtattggaccactttatagt-ttatatgac-acatccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG
     |||   ||| | |    ||      ||  ||   |   |  |  |   | | ||    |   | || ||  |||||     |  |||||   | |||||| |||| ||||| || |||| ||||||| | |||||||| ||||| || |||||||||||||| || || |||||||| | ||||
--agcactataattgaaagtagagtgctttaaattgatgtggaaattagaaaccggcatgaagcttttataaagcattataaacttatttcctttgatacagACTCTAAAAAATGCTTTGTCACAATATAAACTTGGAGGAGCTGCTGGAGGGAGTGATTTTGATCCCAAGGGTAAAAGTGAAAGTGAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G015289_T02 (Zea mays), 3'ss of exon 3
aatatac-tgagattcacatatcagcaaaagaatctggattctga--gctgcatttctgtattggaccactttatagtttatatgacacatccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG
   ||   || ||||  | ||   |    |   | |   ||   |  |||  ||  | | | |  | ||  ||||    |   || |   | ||||  | ||||||||||||||||| || |||| ||||||| | ||||| || ||||| |||||||||||||||||||| ||||||||||| ||||||
-ccatgggtgtgatttgcttaatggatgcattttttatgtttatattgctttatggcagaactttaacatgttatcccatcattgtct--ttcttccatacagACTTTAAAGAATGCTTTGTCACTATATAAACTTGGAGGTGCTGCTGGAGGAAGTGATTTTGATCCAAAGGGAAAAAGTGATAATGAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G51720.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------aatatactgagatt-cacatatcagcaaaagaatctggattctgagctgcatttctgtatt----gg--accacttta-tagtttatatgacaca-----------------tccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG
                                 || | ||  |||| | | |||     |    ||   | || | |  | | ||  | | ||    ||   |||| |||   |||  |||||  ||                 |  |  |  |||||| || ||||||||  | |||||||||||| | ||||| ||  |||||||||| || |||||||| |||||||||||||||||||||
gtactgtgatttccatcagttatattccattatatttcctctgatttctcttatttttcaccttatactgtttgtcattttccttcttctttttcccggttgccaccttaactgttcttatgattcagaattgtaatgggtttttaatctttcgcagACGTTGAAGAATGCTCTGTCACCATATAAACTGGGAGGGGCTTCTGGTGGAAGCGACTTTGATCCTAAAGGAAAAAGTGACAATGAG

upper sequence: GLYMA08G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 3
aatatactgagattcacatatcagcaaaagaatctggattctgagctgcatttctgtattggaccac-tttatagttt-atatgacacatccttc---tctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG
     |      ||  | | |||  |||  ||||  ||        |    || |  || |||  |   || || | | ||||        ||||     |||||||| ||||||||||||| |||||||| ||| ||||||| ||||| |||||||||||||||||||| |||||||||||||| || |||
----cagaacttttggcttgtcaa-aaactaatccagacaggaccttagtcttttagataggaagagacttctattgtgatatcctgagctcttcaatcatgcagACTCTAAAGAATGCCTTGTCACCATACAAACTAGGAGGGGCAGCAGGTGGAAGTGATTTTGATCCGAAAGGAAAAAGTGATAACGAG

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|208082626|gb|GD885168.1|GD885168
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|193529861|gb|FK485710.1|FK485710
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|7924271|gb|AW830297.1|AW830297
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|16997272|gb|BM086644.1|BM086644
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|193578443|gb|FK537663.1|FK537663
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|193399675|gb|FK363522.1|FK363522
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|193604120|gb|FK555529.1|FK555529
EST:     CCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: CCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|207844666|gb|GD816629.1|GD816629
EST:     TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|208225726|gb|GE025893.1|GE025893
EST:     TTCATCCATCAATGAATTTAAGTGTTACCAAGTTCCTTGGTTTTGAACAG                         ACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGA
EST: gi|208167267|gb|GD963057.1|GD963057
EST:     TTCATCCATCAACGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGA-CAG                         AACTTTAAAGAATGCCTT
genomic: TTCATCCATCAATGAATTTAAGTGTTGCCAAGTTCCTTGGTTTTGAACAGgtattatgag ... ttctctgcagA-CTTTAAAGAATGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatttctgtattggaccactttatagtttatatgacacatccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG
                                        catccttctct  CT-rich tract
                    actttatagtttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatactgagattcacatatcagcaaaagaatctggattctgagctgcatttctgtattggaccactttatagtttatatgacacatccttctctgcagACTTTAAAGAATGCCTTATCACCATATAAATTAGGAGGAGCAGCTGGTGGAAGTGATTTTGATCCAAAAGGAAAAAGTGACAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA