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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG

Basic information

species Glycine max
transcript GLYMA10G36210.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 5
-gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgt-taagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
 |||    | | | ||         | | |  | ||||||||  |  |         |||||    | | |       |  | |   |||   |      ||||||||||||||||||||||| | || ||||||||||| ||||| | ||| || ||    ||||||  |||   ||    | | | |       
agcaccgtttgccttctgtgcactgattcg--tgttatttctggacttctggttatagatttcacatcactgactcgcttctctttctttcttttctcctagGAATTATATCATGAATTGCATACTTTGGATAGATTTGAACAAGACTGTCGTCGTAAACAGCAAGAACTGGATGGTTTGGGTTCAAGAG------

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 4
gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgtt---aagtctt----aatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
       || || |  | |  | |  ||  |    || |  |    || | ||| |   ||  ||   | |||||    || |||  |   |   |  |   | |||||| |||| |||||| |||||||  | ||||||||||| |||||||||| ||||||    || ||||||||   ||||| ||     |||||||
------atatac-tgttaactgcatcttactatcaatctgctggcatttatcagttttcttcttttgcatgtcttgttgaaattacaaatttcaatttttttttcagGAACTATACCATGAAATGCATGCACTGGATAGATTTGAACAAGATTATCAGCGCAAACAGCAGGAAGAGGATGGTTCAAGTGTACACCAAAGAG

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G097502_T01 (Zea mays), 3'ss of exon 4
gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattt-tgttaagtcttaatttagtatactt--tttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
   ||  |  |  |  |  |     |   ||| |  | |  | ||  ||   |   | ||    |||  | |  |||| || | | |  |||  ||    |||||||||||||||||||||||||| || ||||||||||| || |||| ||| |  ||     ||||| ||||    |  | | | | |       
--gaatttgtatgtttttgtcatctgccaatt-tggtcttcttattctggttattagtttcacattacttgtctattttgttttcctacttttttgcactcagGAATTATATCATGAATTGCATGCTTTGGATAGATTTGAGCATGATTGTCGTCTTAAACAGAAAGAACAGGATGGCTTGAGTTCAAGAG------

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 4
gcaaaactagacatcctgatggaaagttgattcttatttctt--catgttgaacagc-tgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
   ||  |    ||  |  |     |   |||     |||||    || | |  ||| | |  ||  | | |  |  |||  |      |||  ||    |||||||||||||||||||||||||| || |||||||| || || |||||||| |  ||     ||||| ||||    |  | |   | |       
---aatttgtgtatttttgtcatcggccaatttggccttcttattctggttattagcatcacattacttatttatttttttcttcctacttttttgcactcagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAGAAAGAACAGGATGGCTTGAGTTTAAGAG------

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 4
gcaaaactagacatcctgatggaaagttgattcttatttctt--catgttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
   ||  |    ||  |  |     |   |||     |||||    |||| |  |||   |    |||  | ||  |||  |      |||  ||     ||||||||||||||||||||||||| || |||||||| || || |||||||| |  ||     ||||| | ||   ||  | |   | |       
atgaatttgtgtatttttgtcatcggccaatttggccttcttattctgtttattagc--gtcacattacttattttttttcttcctacttttttgcacttagGAATTATATCATGAATTGCATGCTTTGGATAGATTGGAACATGATTATCGCCTTAAACAAAAAGAACATGATGGTTTGAGTTTAAGAG------

upper sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 4
----------gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
            |  ||  ||  |  | || | ||| | || |  |||| | |   || |||||      ||   | |     |  || |  |  ||||   |  ||||||||||||||||||| ||||||||||| || |||||||| |||||||||||||||||| |||| |||||||| || || |||||  | ||| |||
gtatttgtgatgatgacatgatcttgtaattgcaagcttatgcaaatttttacgc-ttaaacag------ttagcagggaaagacataatgcatctttt---ggttgcagGAATTATATCATGAGTTGCATGCCTTGGACAGATTTGAACAAGATTATCGGCGCAAGCTTCAGGAAGAGGATAACTCGAATGCAGCTCAACGAG

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|193570195|gb|FK524874.1|FK524874
EST:     GGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCT                         GAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
genomic: GGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCTgtgagtatgc ... ctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
EST: gi|208233250|gb|GE031915.1|GE031915
EST:     CTAATGACCTTTGTTCAATATACAGCT                         GAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
genomic: CTAATGACCTTTGTTCAATATACAGCTgtgagtatgc ... ctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
EST: gi|6666544|gb|AW278011.1|AW278011
EST:     AGGCAGAGATGGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCT                         GAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
genomic: AGGCAGAGATGGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCTgtgagtatgc ... ctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG
EST: gi|208168740|gb|GD969192.1|GD969192
EST:     AGGCAGAGATGGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCT                         GAATTATACCATGAATTGCATGCCTTAGACAGATTTGATCAAGATTATCGG
genomic: AGGCAGAGATGGTGATGCAACAACTAATGACCTTTGTTCAATATACAGCTgtgagtatgc ... ctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG
                       tcttaat  putative branch site (score: 3)
                                    tactttttcct  putative PPT
            attttgttaagtctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaactagacatcctgatggaaagttgattcttatttcttcatgttgaacagctgattttgttaagtcttaatttagtatactttttcctgagtgcagGAATTATATCATGAATTGCATGCCTTAGATAGATTTGATCAAGATTATCGGCGCAAGTTTCAAGAAGAGGACAATTCAAATGCCACACAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
-caaaact
- - - - - - - cctgatg
- - - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -cagctga