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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctgggtttttctttctgggttattctttgaaaggaacatctagtgcagaagtgtaaattttagtttgagattatgttccatgtcatcctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAACTTGGTCTTATGGAGGCTATTGCAATCCCTCAAGTTGAGTGTTTTGAAG

Basic information

species Physcomitrella patens
transcript PP1S48_37V6.2
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|162198035|gb|FC372062.1|FC372062
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|162217427|gb|FC392895.1|FC392895
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|162198036|gb|FC372063.1|FC372063
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCAC-ACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|162253370|gb|FC429796.1|FC429796
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|37826678|gb|BJ584690.1|BJ584690
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|162253371|gb|FC429797.1|FC429797
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|162217426|gb|FC392894.1|FC392894
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
EST: gi|37848442|gb|BJ606450.1|BJ606450
EST:     GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAG                         GTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC
genomic: GAAGATGCACACTCTTGGCCATGACTTTATTCCTGACCCCATCCACGCAGgttctaaaat ... ctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcagaagtgtaaattttagtttgagattatgttccatgtcatcctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAACTTGGTCTTATGGAGGCTATTGCAATCCCTCAAGTTGAGTGTTTTGAAG
                                        tcatcct  CT-rich tract
           taaattttagtttgag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgggtttttctttctgggttattctttgaaaggaacatctagtgcagaagtgtaaattttagtttgagattatgttccatgtcatcctggttgcagGTGGTCTTCGATATCATGGGATGGCACCACTAGTATCACATGTTTATGAACTTGGTCTTATGGAGGCTATTGCAATCCCTCAAGTTGAGTGTTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG