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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgttataacagtgtttactgtgtaatgttgtgtgtcttggatgcccacactaagc...

Basic information

species Glycine max
transcript GLYMA01G25940.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 5'ss of exon 3
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgttataacagtgtttactgtgtaatgttgtgtgtcttggatgcccacactaagc
|||| |||||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| || ||| |    |   | |  |  |     |   ||   | ||||| || |    |   | | ||  || |  | |   |     | |            
CTGCTAATGGAGTAGTTATTGCCACCGAGAAGAAGTTGCCTTCTATTTTAGTGGATGAAACATCTgtaagtgtgacattactcac-aatttaagctcccttatctgttcatattctggaggcactaa-tgaatactcatattcatacataaag------------

upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G850355_T03 (Zea mays), 5'ss of exon 3
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgtt-cattatt-catgttataacagtgtttactgtgtaatgttgtgtgtcttggatgcccacactaagc
|||| || || || || |||||||||||||||||| |||| ||||| || || ||||||||||| ||  || ||  |    || | |  |   | | ||   |||| || | | |    |   |   | ||    |      ||  |      |   ||     |  
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtacctaagtttttgaattttctctatgccacattcttacctttctctatgataagtgctaaacagatacctgcatgaaaacttttcaggtgca--

upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 4
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgt-tataacagtgtttactgtgtaat-gttgtgtgtcttggatgcccacactaagc
|||| || || || || |||||||||||||||||| |||| ||||| || || ||||||||||| ||  || ||  |   ||| ||  ||  || | | | |   |||| |   | |  |  || | | ||   ||  | |   ||  |   |      ||      
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtacctaa-gtttttgaatt-ttctctatgccacattcttacctttctctatgataagtgctaaacagatacctgcatgaaaacttttcag-----

upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G850355_T08 (Zea mays), 5'ss of exon 3
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgt-tataacagtgtttactgtgtaat-gttgtgtgtcttggatgcccacactaagc
|||| || || || || |||||||| ||||||||| |||| ||||| ||||| ||||||||||| ||  || ||  |   ||| ||  ||  || | | | |   |||| | | | |  |  || | | ||   ||  | |   ||  |   |      ||      
CTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCTgtatgtgtacctaa-gtttttgaatt-ttctctatgccacattcttatctttctctatgataagtgctaaacagatacctgcatgaaaacttttcag-----

upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattat--tcatgttataacagtgtttactgtgtaatgttgtgtgtcttggatgccc-acactaagc--------------------
|| | ||||||||||||||||| || || ||||| ||||| |||||  ||||||||||| |||| || |||| ||  ||    |  | || | | |   | |  |||   |||| | |   |   |||  |   |  |||  | |       ||  |  ||| ||                       
CTTCTAATGGAGTTGTCATTGCAACTGAAAAGAAGTTGCCTTCTATTCTGGTTGATGAAGCATCTgtaagttgataatcaacaagaatattcgtatcattaccatatagccatgctctgtgatgctttcttcgattgtgtaatttagtcaacatctctgacattagttttctcttttgcctgtttcag

upper sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 5'ss of exon 4
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagttta--------ttttccgttattagatccttttttgttcat---tattcatgttataacagtgtttactgtgtaatgtt-gtgtgtcttg-gatgcccacactaagc---------------
|| ||||||||||||||||||| || || |||||| | || |||||||||||||||||| | || || |||||         |||   |  ||||| || ||||   |   |   |  || |||||      | |    ||  || | |  ||   || |  ||  |  |   | | |               
CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCTgtaagtttgatcaactctttatagcaattagttctttttcattctgtgcctgctcgtgttactttcctttcggttgcatagtttcagtaactcctacgaaactaatgtttatctattgtctgtttcag

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|192309680|gb|FG999893.1|FG999893
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATCAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|24206299|gb|BU965552.1|BU965552
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|15204528|gb|BI427296.1|BI427296
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|9564578|gb|BE474087.1|BE474087
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|213598011|gb|DB972199.1|DB972199
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|7924388|gb|AW830414.1|AW830414
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|298198188|gb|HO039727.1|HO039727
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|21602716|gb|BQ613047.1|BQ613047
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|58014614|gb|CX701356.1|CX701356
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|192325446|gb|FK018387.1|FK018387
EST:     GATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: GATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|18690708|gb|BM519556.1|BM519556
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|208121904|gb|GD918927.1|GD918927
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGTGGC
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGTGGC
EST: gi|120494647|gb|EH222814.1|EH222814
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|14258901|gb|BG881809.1|BG881809
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|4313519|gb|AI460638.1|AI460638
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|14259203|gb|BG882111.1|BG882111
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|7925135|gb|AW831161.1|AW831161
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|151406778|gb|EV276593.1|EV276593
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|19269188|gb|BM885444.1|BM885444
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|4397406|gb|AI496403.1|AI496403
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|21889053|gb|BQ742266.1|BQ742266
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|19052912|gb|BM731579.1|BM731579
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|20448816|gb|BQ252940.1|BQ252940
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|192316846|gb|FK010833.1|FK010833
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|192326825|gb|FK018922.1|FK018922
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|21888974|gb|BQ742187.1|BQ742187
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
EST: gi|23735184|gb|BU765862.1|BU765862
EST:     TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA                         GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG
genomic: TCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttat ... ttgattgcagGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgttataacagtgtttactgtgtaatgttgtgtgtcttggatgcccacactaagc

- - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccacac