Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaagcagagtttgtagtagtccatctcatttatggttagtttctatttatcttcaaatgtgatattatttaatgcactattttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA

Basic information

species Glycine max
transcript GLYMA09G34310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 2
------------gttgaagcagagtttgtagtagtccatctcatttatggttagtttctatttatcttcaaatgtgatattatttaatgcactatt-ttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA
            ||| |    |   ||  |  |    |  ||||||     | |  |   ||||       || |   ||   |   | | || |  |  |||  | ||| ||||| ||||||||||| | |||||  | ||| | ||||| |||||||||||||||||||| ||  |  | || || || || 
gtatgttctattgttaacaatgcaattacatgacaaaaaatcatttcctcctcgcattattttaataatgtatcttgcatctatgtttaccctttgatgctgtcttgtgtcagGATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT

upper sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 2
gttgaagcagagtttg-tagtagtccatctcattt---atggttagtttctatttatcttcaaatgtgatattatttaatgcactattttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA
 || ||| |  | | | | | | |   |   | ||   |   | |||||    ||   |||     ||| || | ||  | |  || ||| |||||| | ||||||| ||||||||||||| || || ||||| || || || ||||| ||||| ||||||||||| || ||||| ||||| || 
tttcaaggattgctaggtggcaatgtctacaactttgcaaaatgagttttccatt--tttccgtcatgaaataactt--ttccatactttatgtgatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATT

upper sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ34882 (Selaginella moellendorffii), 3'ss of exon 2
gttgaagcagagtttgtagtagtccatctcatttatggttagtttctatttatc--ttcaaatgtgatattatttaatgcactattttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA
      | |   ||      | |   |||  | | |  ||  ||| | ||  |   |||     | |   | |||   ||  |  || |     | ||| |||| ||||| || || |||||| |  | || || || || |||||||| |||||||||||||| || ||||| |||||||||
------gtaagattccctccactttttctt-tctgtcttttttttttgttgcttgattctgggctaaagctcttt--cgctatggttgtgtctgtatgt-agGACCTGGCTTTCGACTTGTCCTTGGCAGCGCTCCTAGGAGATAACATTTACAACTTTGGAGAACTTCTTGCGCATCCTATA

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|193679414|gb|FK619792.1|FK619792
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCT
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCT
EST: gi|11413942|gb|BF426017.1|BF426017
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGGATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|151394684|gb|EV264555.1|EV264555
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|10709508|gb|BF009232.1|BF009232
EST:     TCTANTTGGCATACACATCANTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCC-TCTCTGCCCTTCTTGGG-ATA-CATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|193321297|gb|FK283627.1|FK283627
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|19269301|gb|BM885557.1|BM885557
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|17518751|gb|BM187793.1|BM187793
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|208073599|gb|GD872780.1|GD872780
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGAT
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGAT
EST: gi|151403199|gb|EV273009.1|EV273009
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|151412996|gb|EV282804.1|EV282804
EST:     TCTATTTGGCATATACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|254334177|gb|GR849095.1|GR849095
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|33388068|gb|CA851275.1|CA851275
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|192328077|gb|FK020380.1|FK020380
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|193706525|gb|FK643624.1|FK643624
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCT
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCT
EST: gi|298190509|gb|HO032630.1|HO032630
EST:     CACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: CACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|120493180|gb|EH221347.1|EH221347
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|19053931|gb|BM732598.1|BM732598
EST:     TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: TCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
EST: gi|8402724|gb|BE058358.1|BE058358
EST:     GGAATCTCTCTCAGATTCATTCAAGCTG                         GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC
genomic: GGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatc ... gatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttatcttcaaatgtgatattatttaatgcactattttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA
                        atttaat  putative branch site (score: 4)
                   atattatttaatgcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaagcagagtttgtagtagtccatctcatttatggttagtttctatttatcttcaaatgtgatattatttaatgcactattttttgtgatttgttagGATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - -gagtttg
- - - - - - - - - - - -ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcac