Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

Basic information

species Glycine max
transcript GLYMA11G08920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
ctttttcatctaatcttcaatt--atatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA------------
            ||   ||||   ||  |   ||     ||             | ||| || |   ||  || || |   | |  ||||| ||||||  |||| ||||||||||| ||||| ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || || || ||||| ||||||||||            
------------attgccaatggaatgaaatgcacccttttttttttccagttctctgagct-tcttttccatcttagtctcactgactaa-cttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
ctttttcatctaatcttcaat--tatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
 | | | |  | ||   ||||   ||  |   ||     ||             | ||| || |   ||  || || |   | |  ||||| ||||||  |||| ||||||||||| ||||| ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || || || ||||| ||||||||||
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagct-tcttttccatcttagtctcactgactaa-cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatct--tttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
 ||| | |  ||      |  || || | |     | ||  |   |   |||  | ||       |||| | | ||   ||  ||||||     ||| |||||| || |||||||||||||| ||  | ||||| || |||||||||||||| || ||||| || ||||||||||| |||||||| ||||| ||||||||||
-tttctgaaatagaacgtatgtaaatgtttttgtcacttttcatttcatcatc-taaaggaatttttttctatatggtactgttactaaatggatttactagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgt-ttgcacctcatactaatct--tttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
   | |  |  ||     |   |   || | |||    |    | ||    || | | |||    |||  |   ||    ||| |||| |     ||| |||||| || |||||||| ||||| ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || ||||| ||||| ||||||||||
---tgttgttgaaatagaatccactcatttaatgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgt-ttgcacctcatactaatct--tttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA------------
           |   | || | || ||     ||   |     | ||    || | | |||    |||  |   ||    ||| |||| |     ||| |||||| || |||||||| ||||| ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || ||||| ||||| ||||||||||            
-----------agaatccactcatttaatgtttgtgatc----ctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcctaggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatctt------ttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
     | || | |   |  ||   ||||  |      ||      ||| |||  | ||  |    | |  |  || |   | |   |||  ||      ||||||||| |||||||| |||||||| ||  | ||||| || ||||||||||||||||| ||||| || ||  ||||||| ||||| || ||||| ||||| || |
-----taatttgaaagtgcatgcaatattgctgctcctttctattttgccatc-taaaaggcatttctccttattactatttactataactttgttgatttgctagGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagtt-ttatgtttgcacctcatact--aatcttttgc-tagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
                | ||  ||||||    |  ||  |  |  ||   | |   || |||||    || ||| | ||     |  |  |||  ||||  ||||| ||||||||||| || || ||| | || || | |||||| ||||||||||| || ||||| || || ||||| ||||||||||| || ||||| ||||
---------------gtaaaccatatataat-tatagggattgtttt--tagtccaaattgtgatcccttttgtatacatgatgttgttgaattgtttgtgtagGTGATAACAAAGTTTTGTTCTGAGAGAATAGCGAGATATGCATTTGAGTATGCGTATCTAAACAATAGGAAGAAAGTGACTGCTGTTCATAAAGCTAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
--ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
    ||  | ||  ||  |    |||   | ||||||| ||    | | | |||||   || ||  ||  ||||||||   |||||  |  || ||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||
gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgc--acagtctgtagtatgtttgtggctcatgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtg--aactgtgagtt--ttatgtttgcacctcatactaatcttttgct-agGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
     ||  ||  || |   | ||  ||     ||| | | |   |  ||   |||  | |||| |  |  || |||  |  ||| | | |       || | ||||||| || ||||||||||| ||||||||||| ||||| || |||||||||||||| || || ||| | ||||  || || || |||||||| || ||||
----atctcctcgtcatgcttcatgcattgtg-gaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgaca--ttgtgaactgtgagttttatgt--ttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
         ||  ||     | || | | | ||    |  ||   ||  |   |||  | || |||| || |||   || |   |  | | ||  ||  |  |||| || ||||| |||||||| |||||||| || |||||||||||||| ||||| || || || ||| | |||| ||| || || |||||||| || ||||
-caagagggcttgtcagtg-tcatgtgtatgatcgtatctgcaggtttcctacttgccatctatgagattgatgagattcctaatggtgccaaaatt--gtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

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|11413754|gb|BF425765.1|BF425765
EST:     ACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAG                         GTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTAT
genomic: ACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAGgtactcactc ... cttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTAT
EST: gi|16348100|gb|BI973695.1|BI973695
EST:     ACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAG                         GTAATAACAAAGTTCTGC
genomic: ACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAGgtactcactc ... cttttgctagGTAATAACAAAGTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA
                                      tactaat  putative branch site (score: 1)
                                            tcttttgct  CT-rich tract
                    ttttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttcatctaatcttcaattatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - ctcatga
- - - - - - - - - - - - - - - - - - - - - -ccttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcacct