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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgtatccttttatctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT

Basic information

species Physcomitrella patens
transcript PP1S9_51V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G08750.1 (Glycine max), 3'ss of exon 2
ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgt--atccttttatctttctcagT---TATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                              ||  |  | | |   ||||   || ||||  |   | ||  ||| |||| |  ||    ||   |     | |   || ||||||||||| || | |||   |||||||||||||||||||||||| ||||||||||| ||   ||  || || |||   |  |||||  |    
-----------------------------gtacttttattctcatttttcaattgctcaattccaacgttcctatttttattaatttaattggatcaacgaatagGTACCATTTCGATGGGACTACTCGCAAATTCTTCGAGGGTTGGTACTTCAAAGTCTCCATTCCCGAACGGAGGCAGAGCTTTTGCTTCATGTATTCCGTC

upper sequence: PP1S9_51V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA06G08850.1 (Glycine max), 3'ss of exon 1
ttcatagtttagatacttgtaaagtaggattaaatcaaattttgattttttgttactcatgtttcatgtagctaattttgt---atccttttatctttct-cagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                                 ||  || |||  || ||   | |     ||  ||||  ||| |||| |    |   || |||   |   || || ||||||||||| || | |||   ||||||||||||||||||||||||  | |||||||||||   ||  || ||||||   |  |||||| |    
-------------------------------gtatttaactttctttcttcaattcatgaattcaatgttcctatttttctcaatttaattgatcaaccaatagCTACCATTTCGATGGGACTACTCGCAAATTCTTCGAGGGTTGGTACTTCAAACTTTCCATTCCGGAACGGAGGCAGAGTTTTTGCTTCATGTACTCCGTC
















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|18360845|gb|BJ192908.1|BJ192908
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100378952|gb|BY986500.1|BY986500
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|162227522|gb|FC403464.1|FC403464
EST:     GCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100402906|gb|BY973411.1|BY973411
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|18354470|gb|BJ186526.1|BJ186526
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
EST: gi|100374390|gb|BY985771.1|BY985771
EST:     GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGG                         TTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA
genomic: GAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAA

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: 31 (upstream exon), 31 (downstream exon)
Score: 13

CCATGTCCATCTCGAACGGAGCCACCGTGGAGACCAAGCCTCGGAAGGCTGAGTACCTGCCTATGCCTGCTGATCGCGCTACACGCACTCCTCACAGCGGgtaagagtga ... tctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgttactcatgtttcatgtagctaattttgtatccttttatctttctcagTTATCATTTCGATGGCACGAGTCGTCGATTCTTCGAGGGTTGGTACTTCAAGGTCTCCATTCCGGAGGTGAAACAAAGTTTTGCTTGGATGTACACGAGT
                        agctaat  putative branch site (score: 13)
                              ttttgtatccttttat  CT-rich tract
                           taattttgtat  TA-rich tract