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

gtaaggatgagtagttttagattttatataatgtaggctacaagaaatttagctatatcttttttggttattttactttgttatactaatggtatctacccttcatttaccaattatttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG

Basic information

species Glycine max
transcript GLYMA02G05350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05350.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaaggatgagtagttttagattttatataatgtaggctacaagaaatttagctatatcttttttggttattttactttgttatactaatggtatctacccttcatttaccaattatttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG
                                ||| |  | |||||       | | ||| |  ||| |  |||||              ||| |  ||  |||  |||    || |  || |||   ||| | |||||||| ||||||| || | |||||  |  || |||||||||||||| || |||||||||||||||||||| || ||||||||||||||||||
--------------------------------gtaagaaagaagaac----aatgtgtctgtgatggatcgtttac--------------ggtttaaactgttc--ttagtgtttgtg-atgttcgggttttt-cagGTGACTTGAAGCCGGGTGATGAAGCTAAGATCACTGGACCTGTTGGCAAGGAAATGCTTATGCCAAAAGACCCCAATGCCACCATCATCATG

upper sequence: GLYMA02G05350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 3'ss of exon 4
gtaaggatgagtag----ttttagattttatat-aatgtaggctacaagaaatttagctatatcttttttggttattttacttt----------gttatactaatggtatctacccttcatttaccaatta--tttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG
|||||  ||   |     || |  |||  |||  |||  || | ||       ||    | |  | | | ||  ||    || |           |||  ||||  |   || |  || || |||   | |  | || ||  ||     | |||||||| ||||||| || || ||||| |  || || || ||||| ||||||||||||||||||||||| |||||||||||||| ||||| |||
gtaagtctgctcaaaattttcttaattgcataggaatccagcccaccttctgatttcaaacagttgtatgggaaatcaatctctcggtgaagacattagtctaagagatgcttctgttaatgtacttttgagctctaaatctcttccatttcagGTGACTTGAAGCCTGGGGCCGAAGTGAAGATTACAGGGCCTGTGGGGAAAGAAATGCTTATGCCAAAGGATCCAAATGCCACAATCATAATG

upper sequence: GLYMA02G05350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 3'ss of exon 4
gtaaggatgagtagttttagattttatataatgtaggctacaagaaatttagctatatcttttttggttattttactttgttatactaatggtatctacccttcatttaccaattatttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG
                                      |   | | | | |||| ||||    | |||  |   |    |      | | |  ||       | ||   || |  |  | |  |||| ||  | |||||||| ||||||| || ||||| || | ||| || |||||||||||||||||||||||||||||||||||||||||||||||  |||| |||
-------------------------------------tttgtatagaatcagctctatcagcatcggtgctacgatggggccgagtttaggaaatgctttgattatcgtcctagcaactctgatccttttgtttcagGTGACTTGAAGCCTGGGGCTGATGTCAAAATCACAGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACTGTCATAATG

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|7796286|gb|AW781683.1|AW781683
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|120496376|gb|EH224543.1|EH224543
EST:     TGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: TGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|120533254|gb|EH261387.1|EH261387
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|12688950|gb|BG155286.1|BG155286
EST:     CACAAATGAAGATGGAGAAATTGTCAACGGAGTCTGCTCATATCTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTA
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTA
EST: gi|151409217|gb|EV279025.1|EV279025
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|213604735|gb|DB956090.1|DB956090
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|209709563|gb|BW661890.1|BW661890
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACT
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACT
EST: gi|192317371|gb|FK007493.1|FK007493
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGC
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGC
EST: gi|213597241|gb|DB962487.1|DB962487
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAG
EST: gi|209705754|gb|BW661422.1|BW661422
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|20812572|gb|BQ297050.1|BQ297050
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAACCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|11413683|gb|BF425694.1|BF425694
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|5058465|gb|AI736876.1|AI736876
EST:     GTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: GTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|13562564|gb|BG550784.1|BG550784
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|192317372|gb|FK007494.1|FK007494
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCTGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|209714818|gb|BW657360.1|BW657360
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
EST: gi|213589650|gb|DB965838.1|DB965838
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCC
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCC
EST: gi|120533554|gb|EH261687.1|EH261687
EST:     CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGT                         GTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG
genomic: CACAAATGAAAATGGAGAAATTGTCAAGGGAGTCTGCTCAAATTTCTTGTgtaaggatga ... ctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactaatggtatctacccttcatttaccaattatttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG
 tactaat  putative branch site (score: 1)
                                  tttatattcctcttt  putative PPT
                   ttcatttaccaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatgagtagttttagattttatataatgtaggctacaagaaatttagctatatcttttttggttattttactttgttatactaatggtatctacccttcatttaccaattatttatattcctctttatgcagGTGACCTGAAGCCAGGAGCTGAAGTAACAATAACTGGACCTGTTGGGAAAGAAATGCTTATGCCAAAAGATCCAAATGCCACCATCATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA