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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

Basic information

species Glycine max
transcript GLYMA09G04270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
-------------------------gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttaga-gtatggaatgat--agGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                         ||||   |  | | ||  |||  | | || | | ||     || |     |||| |  |  |||   |  ||  |||||||  |||||||||| ||||| ||| | ||||||||  | ||||| |||||||||||||||||||||||||| ||||
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctt-tggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
----------------------gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                         || ||  |  | | |||||  | || || | |   |     | | ||       |  | |  | |  ||||||||  | || ||||||||||| ||| | ||||| ||  | |||||||||||||||||||||||||| ||||| || |
gtatgttgaaacaaatgaattaccatgctttgttcaga-ataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
gtttgtttca----tgaatacataattttttttcttggtctgac----------acattgttactgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
|| |||| ||    | | | ||    || ||| ||| |    |           | |||  | |  | ||    ||| | || ||     |||| ||  |||| ||||||||||| ||| | ||||||||| | |||||||| ||||||||||||||||||||||||||||
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
---------------------------------gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                                  |||||| | | |  |||    |     | |   ||       ||| |||  |   |      || |||  |||||||| |||| ||||| || || ||| | ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagt---ttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
----------gtttgtttcatgaatacataattttttttcttggtctgacacatt---gttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
           ||| ||||||  |  | || || ||       ||   | |  ||   | |||||| | |   | | |  ||||||||||| || ||||| ||||| |||||| | ||||| ||  |||||||||||||||| || ||||| ||||||||||| |
gttagtggagttttctttcatata-gcttatttcttaccaaaagttatatatttttaagctactgagtca--ctcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtttcatgaatacata-attttttttcttggtctgacacattgt-----tactgatttagagtatgga-atgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||  |||| ||    | ||| ||   ||||| | ||| |  |   | |     | || | ||    | |     |||||||||||  | ||||| |||||||||||| | ||||| ||  |||||||||| ||||| |||||||| ||||||||||| |
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------gtttgtttca---tgaat-acataattttttttcttggtctgacacattgttactgat----ttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                                                                          |||||  | |   | ||  || ||||||     |   || |   | |||    |  ||     | |   | ||  |  ||||| || |||||||| ||||| |||||| |||||||||||||||||||||||||||| || || || ||||| ||||| |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------gtttgtttcatgaatacataatttttttt----cttggtctgacacattgttactgatttagagtatggaatgat-----agGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                                                                     |||  | | || |  |  || |   |      || |||| | |  |||| | |   |||   | || |  | |     |||| || || ||||||||||| || ||| |||||||||||||||||||||||||||| || || || ||||| ||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtga-gagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtttcatgaatacataattttttttcttggtctgacacattgt-tactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                     ||  || |||| || |||||  ||   |||     |   || | |  |  ||||| ||||||||||| ||||| || ||| ||||||||||  ||||||||||||| ||||||||||| || || |||||||
--------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG

upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtttcatgaatacataattttttttcttggtctgacacattgt-tactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                     ||  || | || || |||||  ||   |||     |   || | |  |  ||||| ||||||||||| ||||| || ||| ||||||||||  ||||||||||||| ||||||||||| || || |||||||
--------------------gttggttgttttcgtttgacaagttacatacatgactcttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
                             tactgat  putative branch site (score: 2)
     ttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcatgaatacataattttttttcttggtctgacacattgttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA