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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAACGATTGTACTTGGTTTTTGAATACCTGGACCTCGACCTAAAGAAGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaatcttttctgcattagcgtgtatgtgttttaggctaaaagctcaaactatacgtcacattataattcggtattggaatactacctcaagatttatagcctctttgggttcatttgtgcctctggttaacagtgagtaaagctttgcgtgcag

Basic information

species Physcomitrella patens
transcript PP1S25_198V6.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S25_198V6.3 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EDP08130 (Chlamydomonas reinhardtii), 5'ss of exon 3
TGAGAAACGATTGTACTTGGTTTTTGAATACCTGGACCTCGACCTAAAGAAGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaatcttttctgcattagcgtgtatgtgttttaggctaaaagc-tcaaactatacgtcaca--ttataattcggta---------ttggaatactacctcaagatttatagcctctttgggttcatttgtgcctctggttaacagtgagtaaagctttgcgtgcag------
 ||    |||||||||||||| || |||| ||||||||| ||||| || ||||| ||||||      ||| || |   |    | |  ||| | |||||||| || |||           |  |||| |     ||    |   ||  || ||     |  || | ||  |   |  | |||          | |||| | | |  || |   | | |||  |  |   || |   |   |||||   |  ||||  | | | ||||| ||        
CGACCGCCGATTGTACTTGGTGTTCGAATTCCTGGACCTGGACCTTAAAAAGCAGATGGACCAGACGCCGAACTTCAGCCGGAATCAGCGCGTCATCAAGgtgtg-ctagcggga---aaacaagcgggggcaggtggcggcaaaagggcgtcgggtgaagcgccgcaggtgggagctgggtgcgtgctgggtgggaagagtgcgacatggggtttcgccg-tcggtaatcttggataaatctgg---atcgtgaccagaaccttgcgcgctcgtgcag

upper sequence: PP1S25_198V6.3 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
TGAGAAACGATTGTACTTGGTTTTTGAATACCTGGACCTCGACCTAAAGAAGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaatcttttctgcattagc-gtgtatgtgttttaggctaaaagctcaaactatacgtcacattataattcggtattggaatactacctcaagatttatagcctctttgggttcatttgtgcctctggttaacagtgagtaaagctttgcgtgcag
 |||||     | ||| |||| ||||| ||||||||| | || ||||||||||||||||||| | |||| ||| | |||||    |||||  |||| || |||||   |  |         |   | |  |   ||| |   |||      |||  | | || |    || |  ||   | ||||  | ||  |||                                                                  
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactc-acactt----tttttctttttttttggtttcctttctcgcag--------------------------------------------------------------
















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|208374284|gb|DC948372.1|DC948372
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|162257042|gb|FC432781.1|FC432781
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|162211257|gb|FC386969.1|FC386969
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCCTGCCCCCAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|208399221|gb|DC916576.1|DC916576
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|162252581|gb|FC428612.1|FC428612
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|162237468|gb|FC412979.1|FC412979
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGC
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGC
EST: gi|162211256|gb|FC386968.1|FC386968
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|162178344|gb|FC355166.1|FC355166
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|208369085|gb|DC944528.1|DC944528
EST:     AGCATAT-GACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|208355812|gb|DC929993.1|DC929993
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
EST: gi|208373750|gb|DC952713.1|DC952713
EST:     AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAG                         ACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG
genomic: AGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGG

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: 28 (upstream exon), 35 (downstream exon)
Score: 14

TGAGAAACGATTGTACTTGGTTTTTGAATACCTGGACCTCGACCTAAAGAAGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaa ... ttgcgtgcagACCTTTCTATACCAGATCTTGCGGGGCATTGCTTATTGCCATGCCCACAGGGTCCTTCACAGAGACTTGAAACCTCAGAATCTTTTGATTGATCGACGTA




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