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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataacactttttctctacatatcttcatttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG

Basic information

species Zea mays
transcript GRMZM2G017654_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 6
----atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataacactttttctctacatatcttcatttgtgtaccctg-cttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
     |||| ||   |    |  ||  | |  | || ||  ||||  |  ||   |  | |   ||| ||||||| |  |||||  |||||  |  ||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||
gaaattatggaaacagagaactgctggaatgaatacctc--ataggcagttatgtaccaaa---tttgtctacatgttctcattaatgtacaatctcttgtttagGGCCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTG

upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataacactttttctctacatatcttcatttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
                                                        |  |||  ||    ||| |  |   ||||         |       |  | |||        |    || ||  |||| |  ||     ||      |||||    || ||||| || || |||||||||||||| ||||| || || ||||||||||||||||||||||| || || || || || |||||||| ||||
gtgggttattcacggtctgagctgtgctgtctaagtttccgttcttttaattatccagctgagttactagtcctc--tagctctacttacatgttgaggggttttccatatgggaaacttcagacctaa-ttcaatgctggttattgtccaaatagGGAGAGGTAAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGTACACCTTATTGGATGGCTCCTG

upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------atatgaa-atatgtatccccctttat-tctaaacttcca-atagaaacataacaataacactttttctctacatatcttc--atttgtgtaccct---------------gcttgtt----tagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
                                 ||||  | |||| |||     | ||| | || |  |  | | | | | |||   |||    ||| | | |  ||   |    ||||||    | |               | |||||     ||||  | || || |||||||| ||||||||||| || ||  ||||||||||||| ||||| || |||||||| ||||| || || || |||||||| || |
gtacactttagccaactacagttacttttatatatatatatatatatatatatatatatatatatatatatatacatagatatagatatatgtatttgtgtgtgaatggttgtggatttgtaagtcataaacctaaaatatgggtttgttgtatcagGGATTGGTGAAGCTTGCTGATTTTGGAGTTGCAACAAAGCTGACTGAAGCTGATATCAATACACATTCTGTTGTCGGAACGCCCTATTGGATGGCTCCAG

upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------atatgaaatatgtatccccctt---tattctaaacttccaatagaaacataacaataacactttttct----ctacatatctt---catttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
                                             | |  ||||  |  ||   |    | | ||  | ||  | | | |   |           | | |||    || ||| |||    | ||  || |   ||  |    ||||    || ||||| || || |||||||||||||| ||||| || || ||||||||||||||||||||||| || |||||||| || |||||||| ||||
gtagaatacttaccctttgggtcgagctgctcttaaattgcaatcttttgaataccttgccgagtaacgtgtcctgtagttttatttgtagattttttgcttttgtgtatctggaactgcatgtctgatgccttgatggaaattgtctaaacagGGGGAGGTGAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGCACTCCTTATTGGATGGCTCCTG

upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataacactttttctctacatatcttcatttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
                                                    ||  ||||   |        |  |   |    |     ||||  | ||||  | || |||||||| || |||||||||||||| ||||| |||||||||||| | |||||||| || || || || ||||| || ||||         
-----------------------------------------------gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTT--TCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------

upper sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ14289 (Selaginella moellendorffii), 3'ss of exon 5
--------------------------------atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataac--actttttctctacata-----tcttcatttgt-------gtaccctgcttg---------------tttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
                                  | ||      ||||  | |  |        |    ||||| |||| |      |  || |  || | ||  |     | || | |  |       ||  | ||||||               || ||||  | || |||||||| || |||||||||||||| ||||| |||||||||||| | |||||||| || || || || ||||| || ||||         
gtggagtgctaactcgatattcacaggtcttggaaggactggcatatcttcatgaacaaggtgttattcatagagacattaagggggctaacatcctcacgacgaaagaggtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 94

GTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGgttaatggct ... gcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

GTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGgttaatggct ... gcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 48

GTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGgttaatggct ... gcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

GTGTTGGAAGGTCTTGTTTATCTGCATGAACAAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGgttaatggct ... gcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacaataacactttttctctacatatcttcatttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
    caataac  putative branch site (score: 84)
                                         ccctgctt  putative PPT
     aataaca  TA-rich tract