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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattgctgaatccctcccaaccgtaggaaattgaataaataaccgctgaaacttcaagagccttttgtacgaagtatgaacgttgtttcaggttcctagcctttaaaatggcgttgtgtctgtcaagtatgtcaagattcttatggttgagctctgacacgtaacctttccggcgtgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGAGAAGGCCTCGAGCAACCGTATCCACGAATGGCATTTACTGGAGATGCTC

Basic information

species Physcomitrella patens
transcript PP1S99_229V6.2
intron # 4
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|208359919|gb|DC934892.1|DC934892
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAANGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208384928|gb|DC903435.1|DC903435
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTACGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208362752|gb|DC950552.1|DC950552
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|100400342|gb|BY954429.1|BY954429
EST:     TCACCTGGATGCTGGCGACAAAATCTGCTTTCG-CAACCTGTATCTCGAG                         TTGAGGTCAACTCCCCGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TCACCTGGATGCTGGCGACAAAATCTGCTT-CGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208367799|gb|DC944045.1|DC944045
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         NTGAGGTCAACTCCCGGACATACCAAAGGNTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|100422429|gb|BY976369.1|BY976369
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|100411668|gb|BY992279.1|BY992279
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|162166628|gb|FC343520.1|FC343520
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|162229838|gb|FC404291.1|FC404291
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208358441|gb|DC930573.1|DC930573
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208396585|gb|DC915897.1|DC915897
EST:     NTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208392227|gb|DC929488.1|DC929488
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208369415|gb|DC948181.1|DC948181
EST:     TTCACCTGGATGCTGGCGACAAAATCTGNTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|162167044|gb|FC342506.1|FC342506
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208367777|gb|DC944023.1|DC944023
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|100355071|gb|BY964986.1|BY964986
EST:     TTCACCTGGATGCTGGCGACNAAATCTGCTTCCGCAACCTGTATCTCGAG                         GTGAGGTCA-CTCCCGGACAT
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACAT
EST: gi|100372654|gb|BY948639.1|BY948639
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCNAACTCCCGGACATACCGAANGCTGCGTAACGTATGTCACTGG
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTC-AACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGG
EST: gi|100391246|gb|BY971560.1|BY971560
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGA
EST: gi|208390552|gb|DC937484.1|DC937484
EST:     TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAG                         GTGAGGTCAACTCCCGG
genomic: TTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGTATCTCGAGgtactattgc ... tgtgacgcagGTGAGGTCAACTCCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaagattcttatggttgagctctgacacgtaacctttccggcgtgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGAGAAGGCCTCGAGCAACCGTATCCACGAATGGCATTTACTGGAGATGCTC
                            acgtaac  putative branch site (score: 3)
      attcttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattgctgaatccctcccaaccgtaggaaattgaataaataaccgctgaaacttcaagagccttttgtacgaagtatgaacgttgtttcaggttcctagcctttaaaatggcgttgtgtctgtcaagtatgtcaagattcttatggttgagctctgacacgtaacctttccggcgtgtgacgcagGTGAGGTCAACTCCCGGACATACCGAAGGCTGCGTAACGTATGTCACTGGAGAAGGCCTCGAGCAACCGTATCCACGAATGGCATTTACTGGAGATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG