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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgagaacgaacgcaaaaccccctttggcttttagcttcatagatctccacactggatgtgccttcagtgcccaacgagttgcaacctgatcgtggatgtggcacccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGAGGGGGCGGTGTTGATACGCGACGAGGTGGAGATCGTGAACAAGGTCATG

Basic information

species Physcomitrella patens
transcript PP1S336_61V6.1
intron # 6
splice site 3'
intron type U2

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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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgccttcagtgcccaacgagttgcaacctgatcgtggatgtggcacccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGAGGGGGCGGTGTTGATACGCGACGAGGTGGAGATCGTGAACAAGGTCATG
                          acctgat  putative branch site (score: 4)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcgagaacgaacgcaaaaccccctttggcttttagcttcatagatctccacactggatgtgccttcagtgcccaacgagttgcaacctgatcgtggatgtggcacccgtgcagGTGTGATATTGTGTACGTGCTGTTGGAAATGGACCGGATCCTTCGACCGGAGGGGGCGGTGTTGATACGCGACGAGGTGGAGATCGTGAACAAGGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC