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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCGCAATCTTCTCGTCAGTGCATTTCGTTCTGGCGCAGTTGCCGAACTTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggtcattgaatgctgttgcaatcggcatcaggttggtcggtagtatcgacaacgactcccttaacctatcgatttgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S5_176V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_176V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATCGCAATCTTCTCGTCAGTGCATTTCGTTCTGGCGCAGTTGCCGAACTTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggtcattgaatgctgttgcaatcggcatcaggttggtcggtagtatcgacaacgactcccttaacctatcgatttgtgtgcag---------------
|||||     ||||     ||| |||||| ||||  | ||| | || |||||||||||| ||||||| |||||| ||||||||||  |||||||  |  ||| | ||  |||    |   | |  | | |   || |  ||     || | ||| ||    | |   ||||   ||||  || |  |                  
GGATCCTCGGCTTCGGTGGAGTCCATTTCATTCTCTCCCAGCTCCCTAACTTCAACTCCGTTGCCGGAGTCTCCCTGGCTGCCGCCGTCATGTCTCTCTGgtcactc--tcacc--accttatcacca-caatattattttaccgtgttgaatcaacttaaaatttgttaagagatcgtattttcagtttttggaaaaacatgac
















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|162264617|gb|FC440900.1|FC440900
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|208374775|gb|DC932044.1|DC932044
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162250920|gb|FC425742.1|FC425742
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162151884|gb|FC328130.1|FC328130
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|100402500|gb|BY954867.1|BY954867
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|208384180|gb|DC911288.1|DC911288
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162260735|gb|FC435387.1|FC435387
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|100385223|gb|BY950815.1|BY950815
EST:     TCAACTCCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTC-AGCTTTCTACGGC-ATAAGAAAAC
genomic: TCAACTCC-ATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATA-GCACAC
EST: gi|67717986|gb|BJ968245.1|BJ968245
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGGCCATTCCAGCTTCCTACGGCCATAGCAC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGG-CCATTCCAGCTTCCTACGGCCATAGCAC

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: 31 (upstream exon), 35 (downstream exon)
Score: 10

GGATCGCAATCTTCTCGTCAGTGCATTTCGTTCTGGCGCAGTTGCCGAACTTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACCCCTCGTCGGCCCCGTAAACTACAAGCTCCCGGTTCAGTCTGTGTCAGCG




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