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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtactttctattgccctcattgttgctattggagtcagtcagctctcttgtcactaactaaattatccagagtcatcttaaaatgtgggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGTGCCATGAGTGGTCTCACTGCGGATGCTCGCACACTTGTTGAACATGGCC

Basic information

species Physcomitrella patens
transcript PP1S69_9V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_9V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ13773 (Selaginella moellendorffii), 3'ss of exon 3
ttatgtactttctattgccctcattgttgctattggagtcagtcagctctcttgtcactaactaaattatccagagtcatcttaaaatgtgggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGTGCCATGAGTGGTCTCACTGCGGATGCTCGCACACTTGTTGAACATGGCC
                       |   ||    || | ||  ||   | | || |  ||  ||  ||       ||   |||        |  |||  |||| ||| ||||||| |||||||||||||| ||||||   || || |||||||| ||||| || |||| ||| ||||||||||| || || || ||||  |
----------------------gtcagtg--gctgaaatccttcgttttttttctttct--cttgat------aaggtttctc-------gctctttcagGAGCCCGCCAGTGTGGAGAAGATCATGGAGATCGATACGCACATAGGGTGTGCTATGAGCGGCCTCATTGCCGATGCTCGCACGCTGGTGGAGCATGCAC

upper sequence: PP1S69_9V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ29212 (Selaginella moellendorffii), 3'ss of exon 3
ttatgtactttctattgccctcattgttgctattggagtcagtcagctctcttgtcactaactaaattatccagagtcatcttaaaatgtgggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGTGCCATGAGTGGTCTCACTGCGGATGCTCGCACACTTGTTGAACATGGCC
                 |  |   ||      || |  |   |  ||||| |||    |   |   ||   |  | | ||          |  |||  |||| ||| ||||||| |||||||||||||| ||||||   || || |||||||| |||||||| |||| ||| ||||||||||| || || || ||||  |
---------------gtcagtggctgaaatccttcgcttttttttgctcttttgctctttctt---ttgctcccactgataaggtttctcgctctttcagGAGCCCGCCAGTGTGGAGAAGATCATGGAGATCGATACGCACATAGGGTGTGCTATGAGTGGCCTCATTGCCGATGCTCGCACGCTGGTGGAGCATGCAC
















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|37852229|gb|BJ610237.1|BJ610237
EST:     AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACNTCAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
EST: gi|162189533|gb|FC365755.1|FC365755
EST:     AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
EST: gi|18370147|gb|BJ201749.1|BJ201749
EST:     AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
EST: gi|162189532|gb|FC365754.1|FC365754
EST:     GGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: GGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
EST: gi|37846603|gb|BJ604611.1|BJ604611
EST:     CAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: CAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
EST: gi|37841581|gb|BJ599589.1|BJ599589
EST:     AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTG                         GAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT
genomic: AGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGT

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), 32 (downstream exon)
Score: 7

CTTGGTTCCACGGCAGTGGGATTGAAGACCAAGGAGGGAGTTGTTTTGGCCGTCGAGAAGCGAATAACCTCAGTTTTGTTGgtgagtcgca ... gggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGTGCCATGAGTGGTCTCACTGCGGATGCTCGCACACTTGTTGAACATGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctcttgtcactaactaaattatccagagtcatcttaaaatgtgggcttgtagGAACCCACCAGTGTCGAGAAGATCATGGAAATCGATGAACATATTGGGTGTGCCATGAGTGGTCTCACTGCGGATGCTCGCACACTTGTTGAACATGGCC
           actaactaaattat  TA-rich tract