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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgagaacgaacgcaaaaccccctttggcttttagcttcatagatctccacactggatgtgccttcagtgcccaacgagttgcaacctgatcgtggatgtggcacccgtgcag

Basic information

species Physcomitrella patens
transcript PP1S336_61V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S336_61V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G164916_T02 (Zea mays), 5'ss of exon 6
----------------------GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgta--------cgtcgagaacgaacgc-------aaaaccccctttggctttta----gcttcatagatctccacactggatgtgccttcagtgcccaacg--agttgcaacctgatcgtggatgtggcacccgtgcag--------------------------------
                      ||| ||||| ||||| ||||| ||  | ||||||||||| ||||| || || |||||||||||||  ||||| ||||||||        | | |      ||  |        |||    ||||  | || |    |    || | | |    |     | | ||||  |||  |  |   | |||  | |      |  |  || |  | |   |                                 
TTATTGGCACGTACCATGATTGGTGTGAGGCTTTCTCAACGTACCCGAGGACCTACGACCTCATCCATGCTGATAAAGTTTTCAGCAGTTACCAGGACAGgtaaagaatgcctttgctgtttaattctgctctagaaattttctttaccgttcactaagtcgtatggttttttgtatgatgtcttccttttgtgggcggccttatttggtaacaaggttttaaaatgcccacagcttaagcaagtagatactaactatggagtggtcgcag
















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|67691914|gb|BJ952147.1|BJ952147
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|162259361|gb|FC436226.1|FC436226
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37841635|gb|BJ599643.1|BJ599643
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37844729|gb|BJ602737.1|BJ602737
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37841219|gb|BJ599227.1|BJ599227
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|162259347|gb|FC436225.1|FC436225
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|18338709|gb|BJ170733.1|BJ170733
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37839303|gb|BJ597311.1|BJ597311
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|67699873|gb|BJ960106.1|BJ960106
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37852673|gb|BJ610681.1|BJ610681
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37846475|gb|BJ604483.1|BJ604483
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37850166|gb|BJ608174.1|BJ608174
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|37843528|gb|BJ601536.1|BJ601536
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
EST: gi|18339385|gb|BJ171412.1|BJ171412
EST:     ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG                         GTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA
genomic: ACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGA

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: 26 (upstream exon), 33 (downstream exon)
Score: 4

GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAGgtacgtcgag ... acccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGAGGGGGCGGTGTTGATACGCGACGAGGTGGAGATCGTGAACAAGGTCATG




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