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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG

Basic information

species Glycine max
transcript GLYMA09G37720.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 8
------gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
       | |||||| | | ||  | | |    | |   |||| |   ||   ||  |||  |   | |  |  |  |   || |||||    ||      ||||||||||||| || || || ||||| ||||||||||||||||||||| || || ||||||||||  | || || || |||||||| ||  ||   || ||  
tgtagattgttatatctatcgttggga-ataaatgttttatctgtcattgggaatgaatgctattccttactctagatatgacgactttctgttta-----ttcagGATGTTCACGAGACAGCTGCAGGGGCACTATGGAATCTTGCTTTCTATTCTGGTAATGCTCTCTGTATTGTTGAAGAAGGTGGGGTTCCTATTCTAGTGC

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G028796_T01 (Zea mays), 3'ss of exon 8
gttttatatatt-ttgtctgtatacttttttaccatctttatct---gtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
  ||  |||||  | |   || | | |  |||  |  | |  ||     ||  | | | || ||  |  ||   |  | | |   |  |  |||||||    ||||||||||||| || || ||||| ||||||||||||||||||||  || || ||||||||||  | ||||| || |||||||| ||  |||  |||||  
tattagtatataatagaaagttttcatacttagtacttctgccttggaattggaaacgaaagatgtttgttccttagacaatgactccctgtttccac----agGATGTTCATGAGACAGCTGCAGGGGCACTATGGAATCTTGCTTTTTATTCTGGTAATGCTCTCCGCATAGTCGAAGAAGGTGGGGTGCCTGTTCTTGTAA

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079031_T03 (Zea mays), 3'ss of exon 8
----gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
    || |   |||    || |  |||| |  |     |   |    |||   |     || |   |  ||   |  | | |  ||  |  |||||||    |||||||||| || || || ||||| ||||||||||||||||| ||  || || ||||||||||  | ||||| || ||||| || ||  |||  |||||  
tatagtctataatagaaagttttcatacatagtacttctgccttggagttggaaacaaaaagacatttgttgcttagacaatgattccctgtttccac----agGATGTTCACGAGACAGCTGCAGGGGCACTATGGAATCTTGCATTTTATTCTGGTAATGCTCTCCGCATAGTCGAAGAAGGCGGGGTTCCTGTTCTTGTAA

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G44900.1 (Arabidopsis thaliana), 3'ss of exon 8
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
                  |||     ||| | ||   |   |     || | || | ||||     |||| |      | | | |   ||    |  |||||||| ||||||||||| |||||||| ||||||||||||||||| ||| || ||||||| ||  | || || |||||||| |||||  | || |||||| 
------------------gtaagaactttgagca---tagccaagccatct-tggataatctgatataaaatttcctcaatgtgctggtttttttcccagGATGTACATGAAACTGCAGCAGGAGCTCTATGGAATCTTGCTTTTAATCCTGGTAATGCACTCCGCATTGTTGAGGAAGGAGGAGTTCCAGCTCTTGTTC

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 7
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaa-tcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
                  ||| ||  |||     || ||||  |||   | ||   |   |  ||  | |||   |   |  |||  ||||    || |||||||| ||||||||||| |||||||| || ||||||||| |||| ||| || |||| |||||  | || || |||||||| |||||    ||||||||| 
------------------gtaaacaattt--gtttcgttataagttctcacatcccactcttttgggttaatctgatgcagcttttgcttt---tttccagGATGTACATGAAACTGCTGCAGGAGCTCTGTGGAATCTTTCTTTTAATCCTGGTAACGCTCTGCGGATTGTGGAGGAAGGGGGAGTTGTAGCACTTGTTC

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 9
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
 | | |||| |      | |||  || |   |  |    |||| | |||||   |  || |   | | | ||  | |      |   | |||  |||||||| || ||||| ||||| |||||||| || ||||||||||| |||||| || ||||||||||  | ||||| || ||||| |||||  | || |||||  
atgtgatatttgcatcttttatgtttatgacctgttaaaatctctctatattcatgtaaacagaactgattttgaccatgacgtatatatcctttttcagGACGTCCATGAGACTGCTGCAGGAGCTCTTTGGAATCTTGCCTTCAATCCTGGTAATGCTCTCCGCATAGTGGAAGAAGGGGGAGTGCCAGCCCTTGTCC

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24022 (Selaginella moellendorffii), 3'ss of exon 8
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttc--cactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
                                                  |||| | ||  |   ||   |       || |  || | |      ||| |||| |||||||||||||| || |||||  | |||||||||||||||||| |  | || ||  | || ||||| || ||||  || || ||||| || ||  
-------------------------------------------------gtatgcacaacgcctcttct-tgtgtgtgacatgacattgtgggtgtttttagGACGTTCATGAAACTGCTGCTGGAGCTTTGTGGAATCTTGCTTTCAATCCAGGAAACGCGTTGAGGATAGTGGAAGAAGACGGTGTTTCTGCGCTGGTGC

upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24586 (Selaginella moellendorffii), 3'ss of exon 8
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttc--cactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
                                                  |||| | ||  |   ||   |       || |  || | |      ||| |||| |||||||||||||| || |||||  | |||||||||||||||||| |  | || ||  | || ||||| || ||||  || || |||||||| ||  
-------------------------------------------------gtatgcacaacgcctcttct-tgtgtgtgacatgacattgtgggtgtttttagGACGTTCATGAAACTGCTGCTGGAGCTTTGTGGAATCTTGCTTTCAATCCAGGAAACGCGTTGAGGATAGTGGAAGAAGACGGTGTTTCTGCACTGGTGC

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|26058330|gb|CA801244.1|CA801244
EST:     GAGAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAG                         GATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT
genomic: GAGAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAGgtaacttgtt ... ccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT
EST: gi|6719933|gb|AW307580.1|AW307580
EST:     GAGAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAG                         GATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT
genomic: GAGAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAGgtaacttgtt ... ccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT
EST: gi|193606459|gb|FK557800.1|FK557800
EST:     GAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAG                         GATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT
genomic: GAAGGAGGTGTTGCACCTCTGATTGCACTTGCACGGTCTGAAGCAGAGgtaacttgtt ... ccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG
              tcctgat  putative branch site (score: 3)
                               ctacttttcactttcc  putative PPT
                   attaaattcaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttatatattttgtctgtatacttttttaccatctttatctgtttatatatgtaaaatcctgattaaattcaaactacttttcactttccactttcagGATGTTCATGAAACTGCCGCAGGAGCACTATGGAATCTTGCTTTCAATGCTAGTAATGCTCTAAGAATAGTAGAGGAAGGTGGAGTATCTGCACTTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatt