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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT

Basic information

species Glycine max
transcript GLYMA06G17930.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------gtaagt--ttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaa--tggcattgattctctgttgattccctttt---cagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                                                   | | |  || | | || |    |  | |   || |  |||        || || | ||  |  |   |||||  ||  | |  |    |||  |  || ||||   |||||||||| || || ||  || | ||||| ||||||||||||||||| ||||||||||  ||  | |||||||| |||||   |||| ||||||||||  |
gtatgccatcctgcattatactataccatttttatgcaatgaataatacaattattcattttattttattctcatctgtagctgtaaattaagaccaaatcatcactattcattataatgcaaagtgctacttctaacttgtcaacacctttttattcagCTGGGAAGTCCTCAGTGTTGCTTGATGTCAAACCATGGGACGATGAGACTGACATGACCAAATTGGAAGAAGCTGTGAGGAATGTTAAGATGGAAGGCCT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttc--tccatataccactttgcaatggcattgattctctgttgattccct-tttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
       | | |  | | |      |  ||| |  || |  |  |||| |    |  ||| |  |  |||| |    ||  |||      | || |  | ||| ||||||||||||||| |||||| | ||||| || |||||||| || ||||| ||||||   ||||| || ||||| |||||   |||  ||||||| ||  |
-----catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaa-atctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G031545_T03 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------gtaagtttctttcttgtcactaatt-atctttgaactttatcctgt-gctcttctccatatacca--ctttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                                                                |    ||| |  || |||   |  | |  |  |   | |  ||  |||||  |  |||| | |    |||  ||  |||  ||  ||| |  || |  || ||||||||||| ||||| ||| |  | |||||||| |||||||||||||| |||||||||   |||||||| ||||| || ||   ||| |||||||||||| |
gtatgtcagtgtgcatattttttctgtttcattctctcatcacactgtgttgacatgtgctgacactaatctataatgacacccttggaccactatatcgttttttgaagctctgtttgatatccaaaaacttgtgatttcatcaatcttctttccataca-ttgtcagCTGGGAAGTCATCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGGCT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G153569_T02 (Zea mays), 3'ss of exon 5
-------------------gtaagtttctttcttgtcactaattatctttg--aactttatcctgt-------gctcttctccatataccactttgcaatggcattgattct--ctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                    |  ||||  ||||    |  |   | | |||  |    |||  |||       ||| |  | ||||  | |       |  |||| | ||||  |  ||   | |||| |||||||||||||| || ||| |  | |||||||| |||||||||||||| |||||||||   |||||||| ||||| || ||   ||| |||||||||||  |
gtatgtcagtgtgcatagtttctgttttattctctcaatcacacacccttgctattgctatattgttgttgaggctttgtttcatacccaaaagctttaaagcat-ggttctaacctttccataccttgtcagCTGGGAAATCGTCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGACT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccata-taccactttgcaatgg-cattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
               || | |   | | ||||   ||   |||||  | | |   ||| |      ||| | |   |||    | ||| ||  || | |  ||||| || || ||||| ||| || ||||| | || || ||||| ||||| || |||||||||||||| || ||||| || |||||  ||||||||||||| ||
---------------gtaagtttgtgtttttgcctttacacctgtagtttacgatataatgatgtcttggatttctcatctggtttct-ttcttttcttaatcagCCGGAAAGTCATCAGTTTTGATGGATATCAAGCCGTGGGATGATGAGACGGACATGAAGAAGCTAGAGGAAGCTGTAAGATCCATTCAGATGGAAGGATT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
||||||||   | ||||       || | ||| | |||||         |  |    | |   ||| |   |  |||||  | | | ||   | | |  | |||||| || || || ||| || | ||| | ||||| ||||| ||||| ||||||||||||||||| || ||||| ||||  ||  ||||||||||||| ||
gtaagtttgggttttgtt-----ctacccttgtaatttatatgaa----tgatatgaagatgtcttggatttctcattg--tttttatta--ttcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgt-tgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
     ||  |    |||  ||   ||| |||    |  ||   |  |   ||    | | ||  |||   ||    |  ||| | | | ||  |   || |||||||| || || || ||| |||||||||||||||||||||| ||||| ||||||||||| ||||| || ||||||||  |     || | |||||||||||
----attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ07795 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggca-ttgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                                                 |   |||||  |  || | | ||||   ||    |||  |   |    | |  |||||||||||| || || ||  |||| ||||||||||||||||||||||| ||||||  ||||||||| |  || |||||  | || || |||   ||| |
------------------------------------------------gtaagccata-gcttctcttctatggttcttcgagctcactctctcttttgtatagCTGGGAAATCGTCCGTGCTTATGGACGTGAAACCATGGGACGATGAAACCGACATGGTGAAGCTCGAGGCGGCTGTGAGGGCCGTGCAAATGCCCGGGCT

upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28248 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                                    | | ||   |||  ||| | |||     | | | |      | | ||||| ||       | |  |||||||||||| || || ||  |||| ||||||||||||||||||||||| ||||||  ||||||||| |  || |||||  | || || |||   ||| |
-----------------------------------gtaagccatagcttctcttc-tatttggttcttcga----gctcactctctctt------ttgtatagCTGGGAAATCGTCCGTGCTTATGGACGTGAAACCATGGGACGATGAAACCGACATGGTGAAGCTCGAGGCGGCTGTGAGGGCCGTGCAAATGCCCGGGCT

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|7588414|gb|AW704210.1|AW704210
EST:     AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACNNNNNNNNNNGAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
EST: gi|213617811|gb|DB959395.1|DB959395
EST:     AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACNNNNNNNNNNGAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
EST: gi|9259946|gb|BE348093.1|BE348093
EST:     AGCAGAGGAACGGGCAACTGCAGTGAAGGCATCTACAAAANAAAAAGAGT                         CTGGGAAATCATTCTGT-CTGGTGGATGGGAAACCATGG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCAT-CTGTTCTGTTGGATGTGAAACCATGG
EST: gi|298194444|gb|HO041092.1|HO041092
EST:     AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACNNNNNNNNN-GAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
EST: gi|13790786|gb|BG653377.1|BG653377
EST:     AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACNNNNNNNNNNGAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
EST: gi|7232756|gb|AW568109.1|AW568109
EST:     AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAGAAAGAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
EST: gi|208112180|gb|GD912851.1|GD912851
EST:     ATCT-CAAANAAAAAAGAGT                         CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: ATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
                                     tgttgat  putative branch site (score: 4)
                                ttctctgttgattccc  CT-rich tract
                           attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG