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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagttctcattgtatgatcagatgttacacctctaaatgcttgtacttctgcacagacctctaacttgttgcactcgtttattgaccttaaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGATCTTGCTGCGG

Basic information

species Physcomitrella patens
transcript PP1S169_73V6.2
intron # 10
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|162203186|gb|FC379283.1|FC379283
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|162266559|gb|FC442790.1|FC442790
EST:     CGCTATCANGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATA
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATA
EST: gi|162175454|gb|FC350924.1|FC350924
EST:     GTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: GTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|37832005|gb|BJ590017.1|BJ590017
EST:     ATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: ATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|37822469|gb|BJ580535.1|BJ580535
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|162183680|gb|FC359908.1|FC359908
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|162198129|gb|FC373079.1|FC373079
EST:     CTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|37827542|gb|BJ585554.1|BJ585554
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGA
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCAC-AAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGA
EST: gi|162198130|gb|FC373080.1|FC373080
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|37829602|gb|BJ587614.1|BJ587614
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|37828539|gb|BJ586551.1|BJ586551
EST:     GATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: GATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|67720614|gb|BJ970873.1|BJ970873
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGAAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|162266558|gb|FC442789.1|FC442789
EST:     CAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|162160838|gb|FC337660.1|FC337660
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
EST: gi|208365406|gb|DC950873.1|DC950873
EST:     CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACT                         GACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT
genomic: CGCTATCAGGACATGAGAATACGGTCTGTTCTGTGATTACACAGGCCACTgtaagtcccc ... aaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctgcacagacctctaacttgttgcactcgtttattgaccttaaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGATCTTGCTGCGG
                                   tattgac  putative branch site (score: 2)
                                           ttaaaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagttctcattgtatgatcagatgttacacctctaaatgcttgtacttctgcacagacctctaacttgttgcactcgtttattgaccttaaaatctcagGACCCACAAGTTGTAACAGGATCACATGATACCACAATCAAGCTGTGGGATCTTGCTGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC