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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcatggcagctttgtagattttctattttctcttctgtagagaagagtgctaccatttaagactgttgatgtctgaatttggttgatcaaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGATCCTCGTAAGCGGAAACCAGACATCACTAAGGCTACTAAGCTTCTTGGGT

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 3'ss of exon 11
tattcatggcagctttgtagattttctattttctcttct-gtagagaagagtgctaccatttaagactgttgatgtctgaatttggttgatcaaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGATCCTCGTAAGCGGAAACCAGACATCACTAAGGCTACTAAGCTTCTTGGGT
           |     |  || | || ||  |     |  |      |  || | |    |   |   |   | ||     ||      | |  |||||| ||||| | ||    |        | |||   |||||||||||| |||||||||||| || |||| |||||||| || ||||| |   |  || | ||||
-----------gtaagatgaatatcctgttgccgaacatcattccatgggatgtttctgaatggcatgctaagtttccctgctt------ttaccttgcagTTGATCAACCCAGAGGTTACCGTCACAATGACTGAGAACACTCCTGATGATCCTCGTCAGAGGAAGCCAGACATTACAAAGGCAAAGGAAGTTTTGGGGT
















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|15728950|gb|BI741060.1|BI741060
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTACTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208390897|gb|DC945914.1|DC945914
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|37850860|gb|BJ608868.1|BJ608868
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|67692844|gb|BJ953077.1|BJ953077
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|67697660|gb|BJ957893.1|BJ957893
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208385608|gb|DC948967.1|DC948967
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208371855|gb|DC951847.1|DC951847
EST:     GCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCNGAGACTAAAATCGNTGAGAACACTCTCGATGAT
genomic: GCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|37843082|gb|BJ601090.1|BJ601090
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     GGGAGTTCACCATGTTGGAGCNTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208370456|gb|DC952159.1|DC952159
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|37830721|gb|BJ588733.1|BJ588733
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
EST: gi|208371231|gb|DC956009.1|DC956009
EST:     GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAG                         CTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT
genomic: GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGAT

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: 32 (upstream exon), 33 (downstream exon)
Score: 4

GGGAGTTCACCATGTTGGAGCTTGCTGGCTTAGTCAAGGAGgtaacattca ... caaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGATCCTCGTAAGCGGAAACCAGACATCACTAAGGCTACTAAGCTTCTTGGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagtgctaccatttaagactgttgatgtctgaatttggttgatcaaattgcagCTGATCGAGCCTTCTGCGGAGACTAAAATCGTTGAGAACACTCCCGATGATCCTCGTAAGCGGAAACCAGACATCACTAAGGCTACTAAGCTTCTTGGGT
            atttaaga  TA-rich tract