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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaattcatgctttatcctgaaaccaatgcattttctcataatttgtccctagcttgacaattaacagactcatcactcatgtacatatcattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA

Basic information

species Glycine max
transcript GLYMA12G36990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G36990.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G61510.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------gtgaattcatgctttatc-----ctgaaaccaatgcattttctcataatttgtccc-tagcttgacaattaacagact-catcactcatgtacatatcatttt---acagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA
                                                    | |||  ||  || |       ||||   | |  | |||      ||| ||| | |   |  |  ||  |   |||  || ||||| || |   |  | ||   | |||| ||||| || || ||||| ||||| ||||| |||||||| |||||||| || || |||||||| ||||||||||| ||||| || ||||| || ||||
gttagttttcattcctatttctaggaagttattaataagaagaccaagagcaggatttgtgtcttcttgcctgttgaacagagtagagttttgttatattggtcgcgtttttcaaagatctattcactatatgactcaagtcctatttgtatttggaaagGTCGAACCTGGGCACACAATCCTTGTTCATGCTGCAGCTGGTGGAGTTGGGTCTCTGTTGTGTCAATGGGCAAATGCGCTTGGAGCCACTGTGATTGGAA

upper sequence: GLYMA12G36990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g08480.t01 (Vitis vinifera), 3'ss of exon 3
gtgaattcatgctttatcctgaaaccaatgcattttctcataatttgtccc-tagcttgacaattaacagactcatcactcatgtacatatcatt-ttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA
 |  |    ||| |||  ||||||  | |  |   |  ||| |||||   | ||| || ||  || |   | ||        |  |  | |     || ||||||||||| || || | | | |||||||||||||||||||| ||| |||| || ||||| || |||||||||||||| ||||| || ||||| || ||||
ctccacatttgcatta--ctgaaataattagaagatagcattatttgcatcatagattcactctttaatcattctaaggatctaaatttcttgccatttcagGTTGAACCTGGACACATAGTCCTTGTCCATGCAGCAGCTGGTGGAATTGGGTCTCTATTATGCCAGTGGGCAAATGCCCTTGGCGCCACTGTAATTGGAA

upper sequence: GLYMA12G36990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g08470.t01 (Vitis vinifera), 3'ss of exon 3
-gtgaattcatgctttatcctgaaaccaatgcattttctcataatttgtccc-tagcttgacaattaa-cagactcatcactcatgt-acatatcattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA
  |  |    ||| |||  ||||||  | |  | | |  ||| |||||   | |||  | |||  ||  ||  || |  |   |  |  | |  |||||  ||||||||||| || || | | | |||||||||||||||||||| |||||||| || ||||| || |||||||||||||| ||||| || ||||| || ||||
tctccacatttgcatta--ctgaaataattagaatatagcattatttgcatcatagaatcacacctagtcattctaaggatctaaattgcttgccattt--cagGTTGAACCTGGACACATAGTCCTTGTCCATGCAGCAGCTGGTGGAGTTGGGTCTCTATTATGCCAGTGGGCAAATGCCCTTGGCGCCACTGTAATTGGAA

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|15813075|gb|BI785350.1|BI785350
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAG
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAG
EST: gi|298177857|gb|HO027410.1|HO027410
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|151395021|gb|EV264892.1|EV264892
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|213590530|gb|DB973303.1|DB973303
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|192299645|gb|FG987748.1|FG987748
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|254331742|gb|GR843592.1|GR843592
EST:     ATTCTCAAGGGCATTGACAACTCAGTTTTTGCTTCGGCGCTTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGG
genomic: ATTCTCAAGGGCAT-GACAACTCAGTTTTTGCTTCGGCGCT-GTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGG
EST: gi|298191369|gb|HO038848.1|HO038848
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCTAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|192312797|gb|FK003995.1|FK003995
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|192306490|gb|FG996194.1|FG996194
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|192312798|gb|FK003996.1|FK003996
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|298175464|gb|HO015097.1|HO015097
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
EST: gi|58019861|gb|CX706603.1|CX706603
EST:     TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGCCGCTGTTTCCAG                         GTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA
genomic: TCATTCTCAAGGGCATGACAACTCAGTTTTTGCTTCGGCGCTGTTTCCAGgcaatgtact ... cattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccctagcttgacaattaacagactcatcactcatgtacatatcattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA
               aattaac  putative branch site (score: 2)
                                            tcatttt  putative PPT
                                      tacatatcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattcatgctttatcctgaaaccaatgcattttctcataatttgtccctagcttgacaattaacagactcatcactcatgtacatatcattttacagGTTGAACCCGGTCATACAATTCTTGTCCATGCAGCAGCTGGCGGAGTTGGATCCCTATTGTGTCAGTGGGCAAATGCTCTTGGTGCAACTGTTATAGGAA

- - - tcatgct
- - - - - - - - tcctgaa
- - - - - - - - - - - - ccaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcactca