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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG

Basic information

species Glycine max
transcript GLYMA08G28320.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatg--caaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
     ||      ||  |  ||||  | || || ||  | | ||  |||  ||  ||  ||| |  | |  |  | ||||   ||| |||||||| ||  | ||||| ||||||||||| ||||||||||| || ||||| || ||||| || || || ||||||||  |||||||||| || ||||||
--gtaaaggcgcatagcttctatttgtata-atatt--tttttatgtttccaagtttagtttcagttttgagatcgaacttgctgtgtagGTTGGCCCAAGGTTCTGTTTGAACCCAATCAAAATATTTGGCGGTAGTTTCGGTGGCCCTACATTGTACGAGAATCCATTCTATGTGTCTCCCAATCAG

upper sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
||      ||||   ||   ||| |||   |  | || |  |||  ||| |   | | ||  ||  |||      | | || | | |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |                                   
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATG----------------------------------

upper sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtt-tagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
||      | ||   ||  |||| |||    |  | | |  | |  ||| ||  | | ||  ||  |||      | | ||  || |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  |||||||| ||   |||  | || || ||||||
gtaactgcactgagcttctttatggatactcaggt-gcttcccagttttgtataaataat--aaattgtgc-tggattgctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG

upper sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
||      ||||   ||   ||| |||   |  | || |  |||  ||| |   | | ||  ||  |||      | | || | | |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  |||||||| ||   |||  | || || ||||||
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG

upper sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 6
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctg-tatgcaaactacttgtt--tagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
||  ||||  || |     ||  |||||       | ||||     || | |||| |  | || | |  | |   ||||  |||||  |||||||||||  |||| || ||||| || || || |||||||||||||| |||||||||||||| ||||||||||||||  | ||  | ||||| ||| ||
gtttgaaa--tgattcacctttctgattatagaacttatctagttgttgtaaataat--tctagcttaatcttggaactggttgttgatagGTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG

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|151406729|gb|EV276544.1|EV276544
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|10253404|gb|BE821170.1|BE821170
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|13789330|gb|BG651921.1|BG651921
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|151396331|gb|EV266208.1|EV266208
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|51342958|gb|CO983700.1|CO983700
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|151412110|gb|EV281922.1|EV281922
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
EST: gi|58018455|gb|CX705197.1|CX705197
EST:     AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAG                         GTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AGTCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATTGAGgtccgaaaat ... acttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG
                         atttaac  putative branch site (score: 3)
                                              cttgttt  putative PPT
         taaatttttaatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactacttgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG