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'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga...

Basic information

species Physcomitrella patens
transcript PP1S408_23V6.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 19
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||| |  ||| |||||| | |||||  | | |     |  | |    | |  || |   | |   |  ||  ||   ||  |  ||| |  ||                      
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATATATGgtaatattcatgatcttatattggttattacgtactaattatttaccatgtatattctaagccgttgatttgaatgcag----------------------

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcat-tttttaaatgga--ggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||  |  ||| |||||| | ||||| |  ||| |  |     ||||    ||   |||   | ||        ||   || |   ||||                             
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag--------------------------

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GRMZM2G059381_T01 (Zea mays), 5'ss of exon 19
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcattttttaaatggag--gaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    |||||  | || || |  ||| |||||| | |||||  ||| |   |||  |||  |  | |    |      |||    ||||     | || ||                                
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATATATGgtaatattcatgctttcatctgagctgaaagcaccttcgtgtacatcttaaggttgttgatctggatgcag--------------------------------

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
|||||||||||||||||||| ||||| ||||||||||| || |||||||| || ||||| |||       |    ||  |  | ||||| |   || |||||| |   ||   | |     |  || ||    | | |  | || |  || || |        ||  ||||         || |||||  | || |    
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtgtgatcgtttgtactagct--------tgctgatg--------cttcttttttgtttgtag---

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 19
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
|||||||||||||||||||| ||||| ||||||||||| || |||||||| || || || ||        |    ||  |  | || || |   || ||||||||   ||   | |     |  || ||    | | | ||  | |  || || |        ||| ||||  |     |||||| ||  |         
AAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTATATGgtatggaaataaatcattcccacaaattcagtgtgtgtggtcatttgtactagct--------tgttgatgcttc----ttttttctttgtag-------

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga
||||| || ||||||||||| |||||||||||||| || || ||||| || |||||||| ||   |    |    ||  |  | ||||| |   || |||||| |   | |    | ||     || |||   |||| | |  |     |    |||   |      |||||                            
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatg---agattttacaaatctctctttcatcttttgcctgctgactgcttatttctctgatgatag-------------------------

upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
lower sequence: EDP05282 (Chlamydomonas reinhardtii), 5'ss of exon 11
--------------------------------AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcattttttaaatggaggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaa----gatttttttttcatctgaaatga--------------------------------
                                ||||| ||||| ||| |||| || || ||||||||||| || ||||||||||||||   ||||   ||| ||       || || ||||  | |     ||   |      ||      |  |  |   |||  | | |||   ||||    | ||   ||  ||  | ||  ||      ||     |   |     | |                                   
AGGGCGGTCGGCTCAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTGGCGCAGGGCGAGTACATTGCGCCAGAGAAGATCGAGAACACCTACA--CGCGgtgaga--gtagcatagtgcgagaggggcggggcggggcagttagggtcgctgctaggtttcggtccgtgt---ctaaggcggctg-ggctaatgcggctggatttgtgccgacccagtccccgctcaacaccccgcccctctgcgcccgcccccccaccccgcag

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|67579410|gb|BJ951531.1|BJ951531
EST:     GCAGTCGTTTTCATAACACAGTGTTAACATACATG                         GTGATAGTTTCAACTCGAGTCTTNTGGCAGTTGCTGTCGTTGATCCAGAG
genomic: GCAGTCG-TTTCATAACACAGTGTT-ACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAG
EST: gi|67578962|gb|BJ951113.1|BJ951113
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|162171191|gb|FC346362.1|FC346362
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACACACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|162269122|gb|FC444990.1|FC444990
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|19778765|gb|BQ039356.1|BQ039356
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTTCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|37848450|gb|BJ606458.1|BJ606458
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|162205653|gb|FC381881.1|FC381881
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
EST: gi|162163688|gb|FC340287.1|FC340287
EST:     CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATG                         GTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA
genomic: CGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGA

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: 8 (upstream exon), 30 (downstream exon)
Score: 3

AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgtatgttcat ... atatgcacagGTGATAGTTTCAACTCGAGTCTTGTGGCAGTTGCTGTCGTTGATCCAGAGACTCTGTCTGCCTGGGCAAAATCGAGGGGTATGAAG




<











<


<