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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC

Basic information

species Physcomitrella patens
transcript PP1S109_214V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaat-ttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                                           ||    |  ||       ||| |||| |    ||||    ||  |  ||   | | | |  |   | | || |   | | |    | ||  ||||    | |   || |  |||| || ||  |   ||| || ||    |  | |   || ||||| || ||||||||||| ||||||||||||||||| || ||| |||| ||||
-----------------------------------------gtatcacctagctatt----ttagagtttctttcctttcgagtttcacgttggtagagtttatt---gttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                                               |   |||       || || ||  ||| |||   || || |||  ||      | |    |||| | |    |||      | |    |     | ||| || | ||||  ||||| ||   |||  ||||||  |  | |   || ||||| || ||||| ||||| |||||||||||||||||||| ||| | || || |
----------------------------------------------gtaccactttg----ttctatttcaccaactta--caatgcattctacttccctttcacctgcttcctgagcacaacat---cccatcatctcttttctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                                      |  |  || | ||  | || | ||| |       | ||||| |  |||   || | |   ||| || |   ||   |  |  ||   ||| |  || |  | |      || ||||||| || ||  |   |||  ||||    |  | |   || || || || ||||| |||||||||||||||||||| ||||| ||| |||| || |
------------------------------------gtatcaccttttctgttt-cacacatttt-----ttcctctttctgcttg---ttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtca------agGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 11
------------------gtgcttatagatttatctctttctactatcaa-atgttcactaaattctgtgact---------gcaaaaattatagttacccatctttttcattga---atttcacacaatgtgcttgggcttacagtattcaatggtta-ctcggtgttataatcctgca-gATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                  ||  || |   | ||| |  | |   ||| || || ||   | || | || | ||         ||| | | |    |||  ||| || ||| |  |   ||  |  |    | |  ||  ||| |  | |    | | || |   || | | |||| | || | |||| || ||||| ||| | || || || | || ||     ||| | ||||||||||||||||| || ||||||||||||||||| ||| | || ||||
gtattgtacttcatttctgtttttctgtttctatttgatacctgtattaatatattattttaaatttgagtcttttcttgttgcatatagttcccttatacattttcttcttaaaggtatcccttaggtggggactgcactttctctttcttttagataacattgtttaaaaatctttcaagGTTGTGGCTATTGCAACTTCCGCACTAGAAGGGTTTAAGAATGAATCGAAGAAAATGGTTGTTGCACTCGTTGATATGGAGCGTGCTTTTGTCCCACCTC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                                                                    || |  |  | | |  | | || ||   ||  || || |  ||     |||   | | |  |   ||||  |||  |  ||||||| || ||||| | | | || || || |  | || |   ||| | || |||||||| ||||| || ||||||||||||||||||||| |||| || |
-------------------------------------------------------------------gtaacattgatgtgctgtaacttacatgtaacttggtttgtttttagaaattaccttgctcatt--tgttgcaatttt-tagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCACCAC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
------------------------------gtgctt-atagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtat-tcaatggttactcggtgttataatcctgca-gATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                               | ||| |||  | |||   | | |  | | |||| || | |   || | |   |||| | | |    |||  ||| || ||| |  |  |   | | | |||   |||  | || | | ||  |  | ||   || | | |||| | || | |||| || ||||| || || ||||| || | || ||     ||| ||||||||||||| ||||| || ||||||||||||||||| ||| | || ||||
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaat-ttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtg---gggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggt-gttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
                                                                    || | ||  | | |  | | || ||   ||  || || |  ||  || | | |    || |||  | |||  |||  | |||||||| || ||||| | | | || || || |  | || |   ||| | || |||||||| ||||| || ||||||||||||||||||||| |||| || |
-------------------------------------------------------------------gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaattatc--ttgctcatttgttgcaatttt-cagATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC

upper sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
||  | ||      |   ||  |   | |    | || |  | ||||  |   |  | |  || || ||    || |||    || || ||       ||   || |   ||||  | ||| | || |     | ||| |      ||| |||| || |||||  || |||| ||||| | || ||     || |||||||||||||||||||| |||||||||||||||||||||||| |||||||||
gtaatcatgctgcaaatgctgcccctttttt--tttttaagagattccctcctttgatatgtt-taatttgatatttttcaagttcaagtttgt----tggcttttgtggtaca--actcacttgtcataaatttttaaac-----cagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC

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 1 RNA-Seqlibrary.


Block sizes: 32 (upstream exon), 30 (downstream exon)
Score: 10

GTTCACCGTGTTCTTGTCGATATTGTTTCTGGTGCCGCAAACGGGACTGCAGGGTTGGGACGATACTCCCCTCTGAAGAGAGAGgtgcttatag ... aatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC
            ggcttac  putative branch site (score: 10)
                                       tgttataat  TA-rich tract