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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA

Basic information

species Glycine max
transcript GLYMA04G39690.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 3'ss of exon 9
gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA-TTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA-
                             | ||| |  | |   |  |    ||| |  || |  | ||   |||   |     | | | ||  | |||| || |  |  |  |  | |   | | |||| ||||| ||||| ||||| |||||||| ||||| ||||||||||| ||  | | || || |    |   ||    |  || |     |      || |  
----------------------------gtaggcattcttcaactactaccatgtttcgctgccatgatctatctttttt----taggggatatctcctaata-ttaatttgggaggctttgtgc-agGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAGGTATATTGTAGTGGTCACGTTCTGCAA--ACCTGGAAGGAGGTATGAGCTA

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 9
gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA-
                             |  || | |  |     |  ||||   ||  |||       |  ||   |   ||||  |  | ||    ||| ||     |||  || |      ||||||||||| ||||| ||||| ||||| |||||||| ||||||||| ||||    ||   |    |  |||   ||  ||   ||||||||||| |    | 
----------------------------gtatgcattagaccagcatgatgttacattgttacacac---ccactgggtgggtgttagg--ttccttgcactgatt----tattgtgctttcgtgcagGAGCATGAGCTTGACGATGAGGACGTCGTTCAGATCATCAAGAAAATATAGGC-GTATCATGTGGTGGAACGAAACCTGTTTTTTTCTGCAAAACTGGGAG

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 9
gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATT-----TGTTATAATCAG--AAGAATCCAAGATGACGTTTTCTGCAAATCGATCA
                                         |  || | ||    |  ||||   | ||  |  |  |   || |||    |   |  |   | | |        | ||||  |||||||||||||||| ||||||||||| || |||||||||||||| || || | | |       ||| ||||||  |   |||||   |  ||| | |    |        
---------------------------------------gttgattctatgaaccgactctataataatcttcatttcgttttattgtatctcttaatttacatttggtgc---cttttgcaaaccagGAGCATGAACTGGAAGATGAAGATGTCGTTCAGATTATCAAAAAGGTGTGAGTGTAGACCTTAAAATCAGTCACATATCCACATTTGCGTGTCCAAGGAG-------

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ34569 (Selaginella moellendorffii), 3'ss of exon 8
gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA
                                                            ||  ||  || |||| | |  || ||| || | | | |   ||       | ||   ||| |  ||||||||| ||||| || ||||||||||| ||||||||||| || ||  | |||                                                 
-----------------------------------------------------------gtatgttagttgttcttctttgtttttgcgcct-cgatcgtttagaaagcctctgcctttgtt--ccagGAGCACGAACTAGACGATGAAGACGTGGTTCAGATTATTAAAAAGATCTAA-------------------------------------------------

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|120532810|gb|EH260943.1|EH260943
EST:     AAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: AAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|193543326|gb|FK502505.1|FK502505
EST:     GCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: GCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|14991431|gb|BI317104.1|BI317104
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|58024862|gb|CX711603.1|CX711603
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|58023958|gb|CX710699.1|CX710699
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|22933763|gb|BU550902.1|BU550902
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|15816018|gb|BI788293.1|BI788293
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|151407189|gb|EV277004.1|EV277004
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|16345802|gb|BI971397.1|BI971397
EST:     CAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|14008785|gb|BG725389.1|BG725389
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|8284564|gb|BE022132.1|BE022132
EST:     GCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: GCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
EST: gi|57575753|gb|CX548728.1|CX548728
EST:     CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAG                         GAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA
genomic: CTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattg ... tgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA
                         tactaat  putative branch site (score: 1)
                                  aaatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatattgtacttaatttactttatttttggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcattgttgagcatgccacctactaatcgaaatatgttgttgcttaccagGAGCATGAACTTGAAGATGAAGACGTTGTTCAGATTATCAAGAAAGTATAATTTGTTATAATCAGAAGAATCCAAGATGACGTTTTCTGCAAATCGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG