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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagctttgtcaggtacattaataaccttttgaaaccattccagaagcttctgtgtttcattgttgggttattaatcctgtctgttgtgcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT

Basic information

species Physcomitrella patens
transcript PP1S84_129V6.1
intron # 36
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_129V6.1 (Physcomitrella patens), 3'ss of exon 36
lower sequence: LOC_Os03g11470.1 (Oryza sativa), 3'ss of exon 14
---ttttagctttgtcaggtacattaataaccttttgaaaccattccagaagcttctgtgtttcattgttgggttattaatcctgtctgttgtgcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT
   | || ||||  |  |  || ||      ||||      | | |     |      | | | ||  |    | ||    ||| | | || | |    |||||| ||||||||||||||||| || ||||||||||| |||||||| || ||| |||| |||||||||   || ||||| ||    ||||||||||| || |
gagtatttgcttgatgggccaccttttgttactttcagtttcctactctgtgtaaacatctct-atcatcaattcatagtgcctttgttttatacc--aacagGGATATCCTGGGAAGTTCTACTGTCCAAGAATGAATAGCATGAATAAACCAGCATATGCAGCAATATGTACTCATTCACCAGACAAACCAGTTCTGATTT

upper sequence: PP1S84_129V6.1 (Physcomitrella patens), 3'ss of exon 36
lower sequence: EFJ04356 (Selaginella moellendorffii), 3'ss of exon 6
ttttagctttgtcaggtacattaataaccttttgaaaccattccagaagcttctgtgtttcattgttgggttattaatcctgtctgttgtgcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT
                                             | |  ||        ||| ||   | || |    |  | || ||   |   |||||| |||||||||||||| || |||||  ||||||| ||||||||||| ||||| ||||| || || | ||| || || || || || || ||| | ||||
---------------------------------------------gtaaattaaacaaaacat-gtactgctactgcaacgctttgctgc-ttactacagGGATATCCTGGGAAGTTTTACTGCCCTCGAATGAATAGCATGAACAAACCAACTTACGCTGCTATCAGAACACACTCGCCTTTGAAGCCGGTTTTGATAT

upper sequence: PP1S84_129V6.1 (Physcomitrella patens), 3'ss of exon 36
lower sequence: EFJ17505 (Selaginella moellendorffii), 3'ss of exon 31
ttttagctttgtcaggtacattaataaccttttgaaaccattccagaagcttctgtgtttcattgttgggttattaatcctgtctgttgtgcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT
                                             | |  ||        ||| ||   | || |    |  | || ||   |   |||||| |||||||||||||| || |||||  ||||||| ||||||||||| ||||| ||||| || || | ||| || || || || || || ||| | ||||
---------------------------------------------gtaaattaaacaaaacat-gtactgctactgcaacgctttgctgc-ttcctacagGGATATCCTGGGAAGTTTTACTGCCCTCGAATGAATAGCATGAACAAACCAACTTACGCTGCTATCAGAACACACTCGCCTTTGAAGCCGGTTTTGATAT

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|162256004|gb|FC431768.1|FC431768
EST:     ACAATTTTAAGCCCAGCGTTCGGCCTGTGCCACTTGAAGTTCACATTCAG                         GGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCA
genomic: ACAATTTTAAGCCCAGCGTTCGGCCTGTGCCACTTGAAGTTCACATTCAGgtacttatta ... gcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCA
EST: gi|162256070|gb|FC431243.1|FC431243
EST:     ACAATTTTAAGCCCAGCGTTCGGCCTGTGCCACTTGAAGTTCACATTCAG                         GGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCA
genomic: ACAATTTTAAGCCCAGCGTTCGGCCTGTGCCACTTGAAGTTCACATTCAGgtacttatta ... gcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCA

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: 10 (upstream exon), 26 (downstream exon)
Score: 2

GGACTTGGCTAACTGGCTTGGAATTGAGGAAGTTGGTCTTTACAATTTTAAGCCCAGCGTTCGGCCTGTGCCACTTGAAGTTCACATTCAGgtacttatta ... gcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcttctgtgtttcattgttgggttattaatcctgtctgttgtgcttggacagGGTTATCCTGGGAAGTTCTATTGCCCAAGAATGAACAGCATGAACAAGCCAACATACGCAGCAATAACAACCCATTCTCCCTTTAAACCAGTTCTTATAT
                          tattaat  putative branch site (score: 2)
                         ttattaat  TA-rich tract