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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCTGGGACGGAGGCTGAACAGGCCGGGAAAGCGTCAGCATGCGAGGGGTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatttgtggttgaattggttgggcgtggatggataaggtgttataattgtgactcaatcaacgatgctaccattatggattattttcttttcat...

Basic information

species Physcomitrella patens
transcript PP1S61_191V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_191V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT5G50960.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTCCTGGGACGGAGGCTGAACAGGCCGGGAAAGCGTCAGCATGCGAGGGGTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatttgtggttgaattggttgggcgtggatggataaggtgttataattgtgactca-atcaacgatgctaccattatggattattttcttttcat-
|| || ||  |  |  | |||   || || ||| |     | || |  || || ||||| ||| ||   ||||||||||||||||||||||| || ||||||  |  ||||    || | |   ||| |  | | |   | |     | |  ||  || ||| |   | |||   |   | |    |  |||| || |  | 
TGCCCAGGTCCTCAATCAGAATCTGCTGGAAAATCAGATTCTTGTGCTGGCTGCCCTAATCAGGAAGCTTGTGCTACTGCTCCTAAAGGACCTGACCCAGgttcg--atttcactttaattactttgtggctaggtttttgaatgtctctgctttcgattcatacttaggattacaatttaaaacttggttttgttgttgtt
















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|100436255|gb|BY961125.1|BY961125
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAACGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|208388173|gb|DC941756.1|DC941756
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|100407338|gb|BY991652.1|BY991652
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|208389876|gb|DC937707.1|DC937707
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|100411911|gb|BY992401.1|BY992401
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|100445148|gb|BY964447.1|BY964447
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|208356420|gb|DC914296.1|DC914296
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|100389931|gb|BY971283.1|BY971283
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|18330296|gb|BJ162302.1|BJ162302
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|100443639|gb|BY963736.1|BY963736
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST: gi|208349798|gb|DC905922.1|DC905922
EST:     GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG                         ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG

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: 34 (upstream exon), 19 (downstream exon)
Score: 5

TGTCCTGGGACGGAGGCTGAACAGGCCGGGAAAGCGTCAGCATGCGAGGGGTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT




<











<


<