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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaacctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

Basic information

species Glycine max
transcript GLYMA11G00600.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
-----------------cta-acctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgt-ttgcccctaaactttggttgctcaaa-atgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
                 ||| || |   |||   |||   |     |  | ||      |||||     | | ||  | || | ||     | ||||    || |      ||  |||| ||||| | |||||||||||| ||||| ||||| |||||||||||  |||| || | ||| |||||||||||||| || ||| | ||||| ||||||    
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgca-gtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 2
--------ctaacctatctgtgattaaac---tttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
        ||||||  ||| | ||| ||    | | ||   ||  |      ||   ||  | || |   |   |  |   |  | |   |   ||  | ||||   |||||||||||| |||||| ||||||| || ||||| |||||||| ||||||||||||||||  || |||||||| || |||||| | ||||| ||||||||| 
gtaaaaaactaaccattcttttatttaataaatctctgagaccaattcatggtttattgtgtttgatcattgtgggatattctaacaaagtatgtgtaccaaattgagcagTTTGGGTACATTGTCCTGACAACATCAGCTGGAATCATGGACCATGAAGAGGCTAGGAAGAAAAATGTTGGGGGCAAAGTGCTTGGTTTTTTCTACTAG-

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------ctaacctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatga--------tgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
                              |||   |      | | | ||| |   ||   ||       || | |       |   |  | ||||    | |  | | |  |     |||||        |||||||||| ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| |||||  | |||||||| |||||| 
gttggcatccaaaacccactattttttttataaaaaaaaaaaaaatgatcttaaaaatgaacttggcaaactgcaaggggccaatcattattctttgagtatgatttcttggggtgactaatgagtgctatttgcagTTTGGATATATTGTCTTGACAACTTCTGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAAAATGTTGGTGGCAAAGTTCTTGGTTTCTTTTACTAGT

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 4
---ctaacctatctgtgattaaactttatgttgccgttattctcttgt--atgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
    | | ||   |   | |  | |  | | |    ||  | |       ||  || |||||||   || |  ||  | |    || | |  |||||   |||||||||| || |||||  |||| || || ||||| |||||||||||||| |||||||||||||||||||||||||| |||||| | ||||||||||||||||
tattttagctgcatactagtgtattacaggctagatttcctttgccaacaatatatgtggtttcatttgatgacctttga----tgatggtccaaaa-attgcagTTTGGATACATTGTGCTGACTACTTCGGCTGGCATCATGGATCATGAGGAGGCTAGGAGAAAGAATGTTGGTGGCAAAGTGCTTGGTTTCTTCTACTAGG

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 2
--ctaacctatctgtgatt--aaactttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
   |||  |  | ||  |        ||  || |    ||||  |||  |  | || ||| | |  |      |     |   | ||| ||        || ||||||| || ||||| |||||||| |||||||| || ||||| || || ||||| ||||||||||| || || || || ||  | |||||||| ||||   
acttaagttgacagtagtgtggggaatttcgtagtgagtattgcctttgactcttagggtatttggttccattctgctgatgctcgtttcttg----tttgtagTTTGGATACATTGTTTTGACAACATCTGCTGGAATTATGGACCACGACGAGGCCAGGAGAAAGAACGTAGGAGGAAAGGTTCTTGGTTTCTTTTACTGAT

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 2
ctaacctatctgtgattaaactt--tatgttgccgttattctcttgtatgcata---tggtttctcctgtttgcccctaaactt-tggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
      ||| ||  ||| |  ||  | | ||| |   |      || |  ||     |||     | | | | | | |  |||| || ||  |     ||  |||||| || || ||||| ||||| ||||| |||||||| |||||||| || ||||| ||| | ||||| || || || |||||  ||||||||||||| |  |
--tctgtatttggcattcacattattgtcttggcaacaagtcaatgaacccacgaattggaagagcatatcttctcatggacttgtgatttttt----tggggcagTTCGGTTACATTGTATTGACGACCTCAGCTGGTATTATGGATCACGATGAGGCCAGGCGTAAGAACGTAGGAGGCAAAGTCCTGGGTTTCTTCTATTGAG

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
------------ctaacctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
             ||| |  ||    |    | || ||||| ||| |  | |   ||||| |  ||   |||  |  |||     |   |||  |   |        |||||||||| || ||||| ||||| ||||| ||||| |||||||| || || |||||||| || ||||||||||| || || ||  | |||||||| ||||  |
aacgatcaagcgttaatcc-tcctcaagaggatttcatgttaccgctgcttttaggtatgaacctgaaatctgattgttg-----agtttttcatcttttt------tgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
ctaacctatctgtgattaaactttatgttgccg-ttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
               ||  | |||  |   |   |   |  ||||  |||| | |   |  |   |||  |    | || ||| |             |||||||| || |||||  ||||||| ||  | |||||||||||||| || || || ||||| |||||||||||||| || ||  | || |||||||| |   
--------------gtttgattttgagagacgaatcgatggcttg-gtgca-aagaagtaacgattttctcttcgatctctggct-------------cagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

upper sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 2
ctaacctatctgtgattaaactttatgttgccg-ttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
               ||  | |||  |   |   |   |  ||||  |||| | |   |  |   |||  |    | || ||| |             |||||||| || |||||  ||||||| ||  |||||||||||||||| || || || ||||| |||||||||||||| || ||  | || |||||||| |   
--------------gtttgattttgagagacgaatcgatggcttg-gtgca-aagaactaacgattttctcttcgatctctggct-------------cagTTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

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|22928272|gb|BU545411.1|BU545411
EST:     GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAG                         TTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
genomic: GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAGgtaaccttaa ... aatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
EST: gi|9439843|gb|BE440356.1|BE440356
EST:     GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAG                         TTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
genomic: GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAGgtaaccttaa ... aatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
EST: gi|16278564|gb|BI942970.1|BI942970
EST:     GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAATACAG                         TCTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAACAG
genomic: GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAGgtaaccttaa ... aatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
EST: gi|7286186|gb|AW598673.1|AW598673
EST:     GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAG                         TTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
genomic: GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAGgtaaccttaa ... aatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
EST: gi|298192624|gb|HO033058.1|HO033058
EST:     GTGTCAAAGAGATTGAAGGTTGGACTGCAATACTACTACCCTCAAGACAG                         TTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG
genomic: GTGTCAAAGAGATTGAAGGTTGGACTGCAAGACTACTACCCTCAAGACAGgtaaccttaa ... aatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG
                        ccctaaa  putative branch site (score: 3)
                           taaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaacctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgtttgcccctaaactttggttgctcaaaatgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - -atctgtg
- - - - - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc