Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgtctatgcggattagttgcacatctcttccttacttctcatacttgttcggtagtcttgctgcaattttctagcatttctgcttaatcttgtgtgcaggatgcgcttgctgttaggtctaacatagttgtggacatgatcgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGAATCCCACCGAGGCAGAGTTGCAGGACATGATCAATGAGGTTGATGCCGA

Basic information

species Physcomitrella patens
transcript PP1S58_258V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_258V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0020g04420.t01 (Vitis vinifera), 3'ss of exon 1
gtatggtgtctatgcggattagttgcacatctcttccttacttctcatacttgttcggtagtcttgctgcaattttctagcatttctgcttaatcttgtgtgcaggatgcgcttgctgttaggtctaa-catagttgtggacatgatcgaatg---acagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGAATCCCACCGAGGCAGAGTTGCAGGACATGATCAATGAGGTTGATGCCGA
                                            | |   || ||     ||| | |   |    | ||  || | || ||  ||||    |      |   ||| | |||  |||   |||| |  || |  || | |||||     |||  |||| ||     | ||  |||  || || || |||||| ||| ||||||||||||||||| |||| | ||||||||||| |  || || ||||| ||
-------------------------------------------gtgagttttctttttgggtcattcc-taggcctgta-tatctttggttcctcttactgg------gtctttgttattatttctgggcatattcatgaa-gtggttgaatgtgtgtagGCTGCATTACCGTAGAAGAATTGGCGACGGTGATTCGGTCGTTGGATCAGAATCCCACCGAGGAAGAGCTTCAGGACATGATAAGAGAAGTGGATGCTGA
















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|162270598|gb|FC446523.1|FC446523
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|18329931|gb|BJ161937.1|BJ161937
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|18359856|gb|BJ191917.1|BJ191917
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|67570099|gb|BJ942923.1|BJ942923
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|162278520|gb|FC453982.1|FC453982
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|18343994|gb|BJ176033.1|BJ176033
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|162244646|gb|FC424613.1|FC424613
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|37853257|gb|BJ611265.1|BJ611265
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|67698429|gb|BJ958662.1|BJ958662
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|37847801|gb|BJ605809.1|BJ605809
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|208362046|gb|DC943487.1|DC943487
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|19790467|gb|BQ041885.1|BQ041885
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|67574994|gb|BJ947818.1|BJ947818
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
EST: gi|162244647|gb|FC424614.1|FC424614
EST:     GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATG                         GTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA
genomic: GATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGA

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: 35 (upstream exon), 35 (downstream exon)
Score: 9

GGTGCTGCGATAAGTTGAGGAATCATGGCGGAGCACTTGACTGAAGAGCAGATTGCTGAGTTCAAGGAGGCGTTCAGTTTATTTGACAAGGATGGCGATGgtatggtgtc ... cgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGAATCCCACCGAGGCAGAGTTGCAGGACATGATCAATGAGGTTGATGCCGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaggatgcgcttgctgttaggtctaacatagttgtggacatgatcgaatgacagGTAGCATCACGACCAAGGAGCTGGGAACAGTAATGCGGTCGCTGGGTCAGAATCCCACCGAGGCAGAGTTGCAGGACATGATCAATGAGGTTGATGCCGA
                     gtctaac  putative branch site (score: 9)
                        taacata  TA-rich tract