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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG

Basic information

species Glycine max
transcript GLYMA20G38230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 4
---------gttccttttttaattcattcttgtaaatt---tgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaat-gcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
         |    | |  || | |  | |  || |||   |||  | || | ||| |   |  ||  | | | ||| |  |||| || ||   |         || | ||||  | ||||||||||||||||| || || || ||  |||||||||||||||| |||||||| ||||| ||||| || ||  | || || |||||  |||  
gtttgggaagacaatatactattgctatttgttacattatatgacctgtttgagtgtt-cactgtgattttctgtta-tatgtgagttcataattctatgacgacatttgcagCTTGAACTGGCAGCATCAGCTTTGTAAGAATCCTCGGCCAAATCCAGATATCAAGACTTTGTTCACTGATCATACCTGCACTCCGCCAAATGGAGCTCGT

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 4
gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
  |       ||||  | |  ||| | ||| |          | ||||  |    | | | |||  | ||||    |   | | ||||  |    |||||  | || |||||||||||||| || || |||||  | |||||||||||||| || ||||||||||| || || |||||| | || ||||||||  |||  
-gtttgaaagtaatctaatgctgttactttaa----cggatattctgtttccattccaatattt--ttagtgtgactgatt-tcccccccaaatgtgcagCTTGAATTGGCAGCATCAGCTTTGTAAGAACCCTCGTCCAAATCCAGATATCAAAACTTTATTCACCGACCATACATGTTCTCCACCCAATGGAGCTCGT

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 4
----gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaat-gcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
    ||| |||||||  ||| |  |    | | || || ||  ||       |  | |   | ||  |  |  |   ||| || | |||   |  ||  | |||| || || |||||||| ||| | ||||| || || |||||||| ||||||||||| ||| |||||||||| ||||| ||  ||| ||| ||||||||||| 
gtgtgtttcttttttctttcctcatgaccattctgtatgtt--gcagatgaggtttggatgacttcgttgttggatgattcat-tgtgcatatgttctcttgcagCCTCAATTGGCAGCACCAGTTGTGCAAGAATCCTAGGCCAAACCCAGATATTAAAACTCTATTCACAGACCACACTTGCACACTTCCGAATGGTCCTCTC

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
  |     | || | |  | |  || |     |     |        |   |  ||| || | | |      | | |   |  | || |  |  ||||||| |||| |||||||| ||||| ||||| |||||  ||||||||||||| |||||||| ||||||||||| || |||||||| ||| | |||||  |||| 
actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgc-cttgcctattttttaatcagtgaattta-----------tctatgc---cccttatcaat--gcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
                                                         |||   || || || |   ||||   |   |      | ||  || ||   || |||     || | ||| | ||| |           | ||||    |  ||||| ||  ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||  | ||||  ||||||||||| |  ||||| |||||  |||  
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatctatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA

upper sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 4
gttccttttttaattcattct-tgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtga-atttatctatgccccttat----caatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
      |||| ||    |  | |||   ||| ||| ||        ||| | |        ||| ||| ||      ||   | |||   || |    |  |||||||| ||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||  | || |  |||||||| |||| |||||| |||||| | |  
------ttttcaacgtttcatgtgttgttttaaatattcttttcattgtacttaatgagaatttaaataagaattgctttcttgtgcttattttgttaccctgcagTCTCAACTGGCAGCACCAGCTTTGCAAGAACCCAAGGCCGAATCCTGACATCAAGACACTGTTTATTGATCACACTTGTGGACCTCCTAATGGTGCCCGT

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|209715994|gb|BW662258.1|BW662258
EST:     ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAG                         TCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT
genomic: ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAGgtatgtgtga ... atcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT
EST: gi|208184069|gb|GD984489.1|GD984489
EST:     ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAG                         TCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT
genomic: ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAGgtatgtgtga ... atcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT
EST: gi|213603698|gb|DB956263.1|DB956263
EST:     ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAG                         TCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT
genomic: ATCTTCCCTACCCTTAAGTCATCAAGACTGCGAACTTTGATCAATCAAAGgtatgtgtga ... atcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG
               ttttaat  putative branch site (score: 3)
                                       ccccttatc  putative PPT
           tattttttaatcagtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
gttcctt
- - - - - - -ttcattc
- - - - - - - - - - - - - - - - - - - agcgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcccct