Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA

Basic information

species Glycine max
transcript GLYMA15G40750.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
ataattacaggt--cttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
    |||  |||  || ||      |  | | |  |||| |        |   |  |  || |    |       |  |   ||| | |    | |   ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||||||||| |||||  | || || ||||||||||||||||||||||| ||||
--ttttatgggtcactgcatattgttttttattttttgatctctcgaagtcaataatgagaaaatattacatatgtaatacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgtt--ttgacatctgt-gtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
    | | | |   ||| |  ||   |   | || |  ||   |   |   | ||  || |||| ||| |     |  |   |||| | |    | |   |||||||| |||||||| |||||||| |||||||||||||| || |||||||||||||| ||||| || || || || |||||||| ||||||||||| || |
--tgtaaaatgctatcatttcaac-ttcttttatgggccactaagactaggtattggtttacatttgttgaagcctgagaaattacctatttcctcttaacagGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttct----gcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
  || |     |||| | |    ||  |  |||||  | ||  ||   || || | |   |  |   ||   | |||||  ||  | || || ||       ||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||| | ||  | || || || |||||||| || ||||| || || |
-aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattg---tatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
--ataattacaggtcttcaatcaaatgctaaatcattgaacatatat---tttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
  ||||||  | || |||||  | |  |||  || ||||| | | ||   ||| | |     || ||   ||| || |||     ||| | | |   ||    ||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||| | ||  | || || || |||||||| || ||||| || || |
gaataattgtatgt-ttcaacaacac-ctatctccttgaatagagatgaatttgtctaacaggaaataattgt-atgtttaacaatacctattc--cttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgac---atctgtgtgatatttgttttta--cttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
                       |  |||    || ||  || | ||| | | |    ||   | |  |  | ||| |||   |    | ||     |||  ||||||||||||||||||||||| |||||||| ||||||||||||||| ||||||| ||||| || || |||||||| || || || || |||||||||||||
----------------------gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
--ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
  ||||  |   || || |  | | | ||||||| ||    |   ||||| | | | || |       ||| | | ||| || | |              ||||||| ||||| || ||||| |||||||| ||||||||||| || |||||||| ||||| ||| |||||||||| ||||| |  || |||||||||||||
gtataaa-atgagttttaacactatttctaaatcttttg-taaccattttctatatgttaatg---aggtgttttgtgtgttgatt--------------agGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
ataattacaggtcttcaatcaaatgctaaatcat-tgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaat-ttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
   | |   |||        || |  | | | || |   ||| | ||  |||| || |  |  ||   |  |  |||  | || | ||    | |||| ||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||| ||  | ||  | || ||||| |||||||  || |||||||||||||
--gagtgagggttgatggagaagtattcattgatgtttccatcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattcttcagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatattt---gtttttacttttccaatttc--tgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
 |||  ||  | ||| ||     | ||  ||       | |||||   |   |||  ||   | ||    | |||   ||||||  |||||   ||||  |  |||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || || || || || |||||||| |||||||| ||||| || ||||
ctaaagacttgactttaa---ggttctggatgtccaggcttatatgcctg--gttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
ataattacaggtcttcaatc--aaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttc---tgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
   |     | | |   ||     |||   |  |  | ||    |   | |  ||| | |  || | | |  | | |||||||  |||| ||  |||   |  |||| ||||||||||| ||||||||||||||||||||||| ||||| |||||||| || || || || || ||||||||||||||||| ||||| || ||||
--gaaggtggctttaagattctggatgtccaggc-ctaaatgcctgggtctactgtctagtgattttttt--tttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
---ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatt-tctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
      | ||||    |    | |  ||     | || | |        |||  |||| |    | | | | ||     ||   |  |||    || | |||||||||| |||||||| |||||||| |||||||||||||| || || |||||||| ||||| ||  | |||||   |||||| || ||||| || || ||||
aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttct----tgtttttaatccggattgaaatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
                                             |   || ||  |    |  || |  |  | | | ||   || | ||    | ||||||||||||||||| |||||||| ||||||||||| || || |||||||| || ||||||||  | |||||   ||| ||||||||||| || || ||||
--------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgtt--cttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

upper sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 3
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
                                          ||  || || |   |    |  || |  |  | | ||||   || | ||    | ||||||||||||||||| |||||||| ||||||||||| || || |||||||| || ||||||||  | |||||   ||| |||||||| || || || ||||
-----------------------------------------gtaagttcttcg---tagttttcgttttcttctagctttt--cttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGTCCGCAGCCGCAAA

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|209719408|gb|BW674488.1|BW674488
EST:     AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|209700869|gb|BW683099.1|BW683099
EST:     AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|192301270|gb|FG990190.1|FG990190
EST:     AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|192298646|gb|FG988557.1|FG988557
EST:     AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
EST: gi|192296353|gb|FG991591.1|FG991591
EST:     AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCG                         GGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT
genomic: AAAACAGCAAGATGAAATTGCTGAGACATGTTTCATTTGTGGATTGTCCGgtaaagtcct ... atttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
        ttttgac  putative branch site (score: 3)
                                     cttttccaatttct  putative PPT
                        atatttgtttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttctgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - gtcttca
- - - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga