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'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

Basic information

species Glycine max
transcript GLYMA13G42800.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
gttagatt-cctgtgtttagataagtgatgaat-----tatgaatttcat------tctactgctttgtcgagttataactggtt-atattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
|| |   |     |||| |||| | | ||  ||     | |||   ||||      |  |||  ||    |   ||   ||| || || | ||   |    | |   ||||| || ||||||||||||||||| || || ||||||||||| || || |||| ||| || |||||||||||  |||||||||||||||||||
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataa-ctggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
          ||   ||   |||    ||||| |||      ||   | || |  | |  || | || ||  |    | |||  ||      |  ||||| || ||| ||||||||||||| ||||| ||||| || || ||||||||||| ||||| |||||| | ||  | |||||||| ||||||||
---------gtgaagtttcgtaacc--tgaatgatggcaaaaatgtcaatgttaagacatgtcacaatctaatgccgtgttaatttcatcttttgcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
---gttagattcctgt---gtttagataagtgatgaa---ttatgaat--ttcattctactg--ctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
    ||   | | |||   |  || |||| ||||||    || || |   | |||   ||     ||||  |      ||||| |   || |  |  ||| |  ||| || | || ||||||||||||||||||||||| ||||| || || || ||||||| |||||||||||||||  |  ||||||||||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatc-catgtgttacttggaactgc-agTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
gttagat-tcctgtgtttagataagtgatgaattatgaatttcattc------tactgctttgtcgagttataactggttatattt-tatgtt--tgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
|| |  | | |  |||| |||||| | ||  ||  |   ||     |      ||   | |  |   | |  |||       ||   | ||||  | || |   ||| | || ||||||||||||||||||||||| || || || || || ||||||| |||||||||||||||  |  ||||||||||||| |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactcaaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
gttagattcctg-tgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
|| || |||||  | ||| ||  || |||  |||  |     |    |  |||||||  || |  ||      |    ||| || |      |  ||||| || ||||||||||||||||| || |||||||| |||||||| |||||| |||||||  |||| |||||   ||| || |||||||||||
gtcagtttcctaatattttga-gagagatacatttgg-----cgagttggtgctttgctgaatggta------ttccctttgtggtcat---tttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttat-attttatgtttgaacatgc--cagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
                    | || | |   || ||       || || |  ||  |   ||  | |  | | |  |  |||||||| | |  |   ||||| |||||| |||||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||| |  ||||||| |||||||||||
-------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gttagattcctgtgtttagataagtgatgaatt--atgaatttcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
|| || || || |  | ||| ||||  |  |    |  | ||  |   |||| || || |  | || |  |     | | ||   ||    |   |||| | || ||||||||||||||||| |||||||||||||| || ||||||||||| |||||||||||| ||||  |||| || |||||||||||
gtgagcttgctttcctcagaaaagtcttacacagaacaacttctacattact-ctctg-catgcta-attttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
-gttagattcctgtgt--ttagataagtgatg-aattatgaatt--tcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
  ||  | |  ||| |   |||     | ||   || || | |   | |  | | || ||| |  | ||  |  ||  || |   |||    |    |  |||||||| ||| | ||||| || ||||| ||||| || ||||| ||||||||||| ||||| |||||  ||||  | ||||||||||| |||||
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttcttta-ttgaacttg--tagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcga-gttataactg----gttatattttatgtttgaacatgc-cagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
 |   |||| |||  ||   ||  || |  |||||    ||  |  |   | |  |  |  | |   | ||      ||||  || | ||  | | |   ||||||| ||||||||| ||||||||||| || || || ||||| || |||||||| ||||| |||||  ||||  |||| |||||||| |||||
atcttattcgtgttatttt-tatctggt--attattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagttgttttgtatcgtttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAG

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|18730643|gb|BM525996.1|BM525996
EST:     ATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG                         CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGT
genomic: ATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAGgttagattcc ... aacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGT
EST: gi|5770902|gb|AI974076.1|AI974076
EST:     ATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG                         CTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGT
genomic: ATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAGgttagattcc ... aacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
                   ttataac  putative branch site (score: 2)
                   ttataactggttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattcctgtgtttagataagtgatgaattatgaatttcattctactgctttgtcgagttataactggttatattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA