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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACTGGGTCCCGAGGACAGGTGACGCAGGTGCGCGTCAAGTTCTTGGATGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattactaaaaccgacacatctttttaatttcctttttggagtgaggttctattaccgaaggtttaattagtctaccaagatcttggatccccgaagt...

Basic information

species Physcomitrella patens
transcript PP1S313_15V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S313_15V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP05500 (Chlamydomonas reinhardtii), 5'ss of exon 3
CGCACTGGGTCCCGAGGACAGGTGACGCAGGTGCGCGTCAAGTTCTTGGATGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattactaaaaccgacacatctttttaatttcctttttggagtgaggttctattaccgaaggtttaattagtctaccaa--gatcttggatccccgaagt-
                     ||||| |||||||||||||||||| |||| || |||||||| || |||||||||||||| ||||| || || || || ||| |  ||    || | | |    |  ||     ||    |||| |  |  |   | | |   |     || | | ||     |     || |  |   ||  
---------------------GTGACCCAGGTGCGCGTCAAGTTCCTGGACGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcac-gcgactgccccgcgctagtatggagctgcccggagggcagagcagcttcggggagccc--tttgccaactggacggagaggggtgtcgacagcg
















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|67721081|gb|BJ971340.1|BJ971340
EST:     TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
genomic: TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
EST: gi|6227301|gb|AW155900.1|AW155900
EST:     TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCANGAAGGTTGCGAT
genomic: TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
EST: gi|162205762|gb|FC382159.1|FC382159
EST:     TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
genomic: TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
EST: gi|162222747|gb|FC399001.1|FC399001
EST:     TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
genomic: TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
EST: gi|7046998|gb|AW476892.1|AW476892
EST:     TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
genomic: TGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
EST: gi|6166867|gb|AW145131.1|AW145131
EST:     CAACGTTAAGGGGCCAGTGCGTGAAG                         GTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT
genomic: CAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGAT

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), 35 (downstream exon)
Score: 18

CGCACTGGGTCCCGAGGACAGGTGACGCAGGTGCGCGTCAAGTTCTTGGATGATCAGAACCGTCTTATCATGCGCAACGTTAAGGGGCCAGTGCGTGAAGgtaattacta ... aatcttgtagGTGATATTTTGACCCTCCTCGAGTCTGAGCGCGAGGCAAGAAGGTTGCGATGAAGAACTCCTATCTCCTATGGCAGGCCACTGGAGCAGTACTGGAAGTT




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