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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcttcctttgactttagatattgaatatgctcaacttacacttaaagttattcatgttcacttaacatttatggaattttatgtttgttttctcgtcacttttctcccatccctagaatttgtcgaagttgaataaatgtgtttgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATGACTTTTGAGTACATTGAAAACTACTGCAAGTCCAAAGCGGGCATGACAG

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 18
lower sequence: EFJ25084 (Selaginella moellendorffii), 3'ss of exon 18
gtatgctcttcctttgactttagatattgaatatgctcaacttacacttaaagttattcatgttcacttaacatttatggaattttatgtttgttttctcgtcacttttctcccatccctagaatttgtcgaagttgaataaatgtgtttgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATGACTTTTGAGTACATTGAAAACTACTGCAAGTCCAAAGCGGGCATGACAG
                                                                                                           |       | | |  ||  | || || |||| |   ||| |      | |||||  | |||||||| ||||||||||||||||||||| | || ||||| |||||  | ||||   | || ||||| ||||||    || | |  |   |  
-------------------------------------------------------------------------------------------------------gtactagcattgtgcttccaagctctccaa-ttgactgcttgtatcc----ttcagCTGGTGTGGGATCGCGCACTTGGTCTTCCAATTGAAAGGCCAAAGAGCATGACCATGGAGTGGCTGGAGAACTATTGCAAGAAGCAAACCGTGACAGCGT

upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 18
lower sequence: EFJ29959 (Selaginella moellendorffii), 3'ss of exon 18
gtatgctcttcctttgactttagatattgaatatgctcaacttacacttaaagttattcatgttcacttaacatttatggaattttatgtttgttttctcgtcacttttctcccatccctagaatttgtcgaagttgaataaatgtgtttgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATGACTTTTGAGTACATTGAAAACTACTGCAAGTCCAAAGCGGGCATGACAG
                                                                                                           | |     | | |  ||  | || || |||| |   ||| |   |  | |||||  | |||||||| ||||||||||||||||||||| | || ||||| |||||  | | ||   | || ||||| ||||||    || | |  |   |  
-------------------------------------------------------------------------------------------------------gtactaccattgtgcttccaagctctccaa-ttgactgcttgtatcgtaccttcagCTGGTGTGGGATCGCGCACTTGGTCTTCCAATTGAAAGGCCAAAGAGCATGACCATGGGGTGGCTGGAGAACTATTGCAAGAAGCAAACCGTGACAGCGT
















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|162176172|gb|FC351914.1|FC351914
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|15320332|gb|BI488151.1|BI488151
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|162165708|gb|FC340889.1|FC340889
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|208386538|gb|DC952747.1|DC952747
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|67697462|gb|BJ957695.1|BJ957695
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|37823157|gb|BJ581223.1|BJ581223
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|208388659|gb|DC953435.1|DC953435
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|37847922|gb|BJ605930.1|BJ605930
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|37835509|gb|BJ593521.1|BJ593521
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|162152561|gb|FC328839.1|FC328839
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|67724660|gb|BJ974919.1|BJ974919
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|162194037|gb|FC370212.1|FC370212
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|208356950|gb|DC922286.1|DC922286
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTTTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|162234310|gb|FC409848.1|FC409848
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|37825198|gb|BJ583264.1|BJ583264
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
EST: gi|162202112|gb|FC378033.1|FC378033
EST:     ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAG                         CTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG
genomic: ACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATG

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: 35 (upstream exon), 29 (downstream exon)
Score: 26

CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCAGgtatgctctt ... tgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATGACTTTTGAGTACATTGAAAACTACTGCAAGTCCAAAGCGGGCATGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctcccatccctagaatttgtcgaagttgaataaatgtgtttgatgtgcagCTCATCTGGGATCGAGCACTTGGTCTTCCAATTGAACGACCGAAGAGTATGACTTTTGAGTACATTGAAAACTACTGCAAGTCCAAAGCGGGCATGACAG
                                          gtttgat  putative branch site (score: 26)
                              ttgaataaat  TA-rich tract