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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT

Basic information

species Physcomitrella patens
transcript PP1S149_289V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 14
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgt--ctggtaatgaattttcaatttgatt--gggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
|| ||| | | | | | | || ||| | | | | | | || | || ||||| | ||||||||| || || ||| ||||||| || ||| ||||| ||| | || ||||||||||||||||| ||||| || || || ||||| |||||||||||
-------gtac-tgtatgtcatcgctgctattttattttctgcagtttactattagcagcatatcaccattgcagagcatcatatctgattctaatttacgtagGTGGTGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTT

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 14
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
||| | | | | | | | ||| | | | | | || | | | | | |||||| | | ||||||||||||| |||||| | ||||| || |||| |||| ||| |||||||||| |||||||| |||||||| || || || || ||||||||||||||
-------------gtaaaatatcaatgctaatagttcaatggttag----ttttacaatctcaaatcagatccgactat-aatttgttctcgcattgcagGTGGTGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTT

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 14
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
||||||| | | | | | ||| || ||| | | |||| ||| || ||| | | || | | ||||||||||||| |||||| | ||||| || | ||| |||| || |||||||||| |||||||| || ||||| || || || |||||||||||||||||
-------------gtagattatt-agcacttgcagttgtatgctgagt---tctaattctacgtcgttcaatcaaatttgatgtgttgtgctttgcgcagGTGGTGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTT

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 14
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
||||||| | | | | | ||| || | | | | | || ||| || ||| | | || | | ||||||||||||| |||||| | ||||| || | ||| |||| || |||||||||| |||||||| || ||||| || || || |||||||||||||||||
-------------gtagattatt-agcactggcagttgtatgcttagttctaattctatgttgttc---aatcaaatttgatgtgttgtgctttgtgcagGTGGTGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTT

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
||| | | | | | | ||| | | | | | || | | | ||| |||||| | | |||||||||||| |||||| | ||||| || ||||| |||| ||| |||||||||| ||||| | || ||||| || || || || ||||||||||||||
-------------gtaaaatatcaactctaacagttcaatggttag----ttttacaatctcaaatcagatccgacttt-aatttgttctcgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 13
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaat-ttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
|||| | || | | | | | | | |||| | | | || || | || | | | || || |||||||||||||| ||||||||||||||||| ||| || ||||| || || || |||||||| ||||| || || || |||||||| ||||| || |
-------gtata-atctatcccaaatctaaaacaaaatttggttgaatcccttaagaaaattgcgtgagaagagaattatattactttgtgtgtattacagGTGGTGGTGTTGCTCTTTTGTATGCTTCGAAAGAACTTGAGAAGCTTTCCACAGCTAACTTTGATCAGAAAATTGGTGTTCAAATCATTCAAAACGCACT

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|162159174|gb|FC334345.1|FC334345
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162198558|gb|FC373404.1|FC373404
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|208356851|gb|DC926862.1|DC926862
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162175003|gb|FC350902.1|FC350902
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162156171|gb|FC332546.1|FC332546
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162192963|gb|FC371946.1|FC371946
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|37850096|gb|BJ608104.1|BJ608104
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162268426|gb|FC444195.1|FC444195
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|208369434|gb|DC955895.1|DC955895
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162276484|gb|FC452682.1|FC452682
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162156170|gb|FC332545.1|FC332545
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|162268425|gb|FC444194.1|FC444194
EST:     TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
EST: gi|208366302|gb|DC947546.1|DC947546
EST:     TGATGCNNTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG                         GTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA
genomic: TGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAA

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: 25 (upstream exon), 31 (downstream exon)
Score: 5

ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTGgtatgtccga ... ggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT
                                    atttgat  putative branch site (score: 5)
 taatgaattttcaatt  TA-rich tract