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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTAATTTGAAGTGAAGGGGATGGCTGAGGCAGTCTTGGAGGGTAGCCAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcggcgcgggttggaagttggggttggttcttggattcggttaagagtagggtttgatggaggcatggcggatccgggttgtgggaaaaggat...

Basic information

species Physcomitrella patens
transcript PP1S246_34V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 5'ss of exon 1
GTCTTTAATTTGAAGTGAAGGGGATGGCTGAGGCAGTCTTGGAGGGTAGCCAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcggcgcgggttggaagttggggttggttcttggattcggttaagagtagggtttgatggaggcatggcggatccgggttgtgggaaaaggat--
               ||  || |  ||| |  || |   ||||||| ||| |||| |||||||| ||||| || |||||||||||||| || ||||| ||||||||  |||  | |   |||  |  ||| |  | ||  |  | || | ||||    | |    || || ||   || |||   | |   |    |  |  
--------------ATGGCGGCGGAGGCGGCAGCGGCGCTGGAGGGGAGCGAGCCCGTGGACCTGGCCAAGCACCCCTCCGGCATCATCCCCACGCTCCAgtaagtcccggatctgcgcggatctgcgggat--tcctgtgggtggggtgagagattcggtccgcggggggatttggggtccttttagcttgttgtgtgttg

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 5'ss of exon 1
-GTCTTTAATTTGAAGTGAAGGGGATGGCTGAGGCAGTCTTGGAGGGTAGCCAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgt----cggcgcgggttgga--agttggggttggttcttggattcggttaagagtagggtttgatggaggcatggcggatccgggttgtgggaaaaggat
 | |        || | |  || |  ||| | ||| |   ||||||| ||| |||| |||||||| | ||| || |||||||||||||| || ||||| ||||||||      || | | |   |||   ||  | |  ||||| | ||   |||| ||  |  |||     ||     | |  |   || | ||| |     |   
TGGCGGCGGCG-GAGGCGGCGGCGGAGGCGGCGGCGGCGCTGGAGGGGAGCGAGCCCGTGGACCTGGTCAAGCACCCCTCCGGCATCATCCCCACGCTCCAgtaagtcccccccgcccccgcccggatctgtatgtgcgggttcatcgagctggttgagtttgaggtggagcggttaactcgtcg---cgcgctgttgatttgg---
















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|18346530|gb|BJ178575.1|BJ178575
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|100438401|gb|BY979938.1|BY979938
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|100441350|gb|BY962639.1|BY962639
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|208354942|gb|DC914206.1|DC914206
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|208376207|gb|DC910783.1|DC910783
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|208373747|gb|DC936560.1|DC936560
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTAGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|7067233|gb|AW497088.1|AW497088
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|208360850|gb|DC934746.1|DC934746
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|100430149|gb|BY978271.1|BY978271
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|100410692|gb|BY992221.1|BY992221
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
EST: gi|18373885|gb|BJ205463.1|BJ205463
EST:     CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCA                         GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT
genomic: CAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAAT

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: 11 (upstream exon), 32 (downstream exon)
Score: 3

GTCTTTAATTTGAAGTGAAGGGGATGGCTGAGGCAGTCTTGGAGGGTAGCCAGCCTGTGGACCTTGCCAAACATCCCTCCGGCATCATTCCTACGCTGCAgtaagtgtcg ... tcttgtgcagGAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG




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