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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccatctcattctatttgcccgttacgcagtggacatcctacaatgaaatctccatatgttgatggttttgaacattatctctagtacgttatctctggtctgaagcttttcactccctaatgacactctcaaccggctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGCCCTTACGATACCCGTGACATTTTTCAGTCATTGGACCTTGCCTGGTCCT

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 14
gtatccatctcattctatttgcccgttacgcagtggacatcctacaatgaaatctccatatgttgatggttttgaacattatctctagtacgttatctc-tggtctgaagcttttcactccctaatgacactctcaaccggctctatg-cagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGCCCTTACGATACCCGTGACATTTTTCAGTCATTGGACCTTGCCTGGTCCT
                                                | || |  |||      |||   |   ||||| |   |  ||   |   |  |  | | ||| |||| ||  |||||| |     || |        ||| ||| ||||  | || |||||||||||||||||||||||||| ||| | |||||  | || || || ||  |||| || |||||  | ||||| ||||||||  
------------------------------------------------gtaaccctcatgc----atgacct--gacattgttattcttaaactccttaattattttaag-ttttaacctcctaatcaactgatctatgaaaaaaatgacagCTGTACCTCGAGTTTCTTGACAAGTTCGAGCGGAAGTTCGTGACACAAGGAGCATATGACACACGCAACATCTTCCAGTCGCTTGACCTCGCCTGGTCAC
















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|208363000|gb|DC946897.1|DC946897
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162186055|gb|FC361883.1|FC361883
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|37828436|gb|BJ586448.1|BJ586448
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|18334455|gb|BJ166472.1|BJ166472
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|37844824|gb|BJ602832.1|BJ602832
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATNTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|37848287|gb|BJ606295.1|BJ606295
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|18339737|gb|BJ171764.1|BJ171764
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162191293|gb|FC366867.1|FC366867
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162158554|gb|FC334557.1|FC334557
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|37823320|gb|BJ581386.1|BJ581386
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162218504|gb|FC395081.1|FC395081
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162191294|gb|FC366868.1|FC366868
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
EST: gi|162185240|gb|FC361750.1|FC361750
EST:     AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG                         TTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC
genomic: AAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGC

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), 26 (downstream exon)
Score: 13

TTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTGgtatccatct ... ctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGCCCTTACGATACCCGTGACATTTTTCAGTCATTGGACCTTGCCTGGTCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctggtctgaagcttttcactccctaatgacactctcaaccggctctatgcagTTGTATTTGGAATTTCTTGACAAGTTCGAGCGGAAGTTTGTGGCTCAAGGCCCTTACGATACCCGTGACATTTTTCAGTCATTGGACCTTGCCTGGTCCT
                       ccctaat  putative branch site (score: 13)