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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcatggttaatgcatcgggtttgttctcttacctgtacattgttattgccgtacgggcttgaaactcattgctccattaattgcctgatttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTTTCAAGAAGATTTACGGTGGCCGTAAGAGCAATGGAGTTAGACCGTCTCA

Basic information

species Physcomitrella patens
transcript PP1S84_153V6.1
intron # 2
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|162242036|gb|FC419409.1|FC419409
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162200859|gb|FC377054.1|FC377054
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|18344903|gb|BJ176944.1|BJ176944
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162200093|gb|FC376555.1|FC376555
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162240450|gb|FC416016.1|FC416016
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|19788851|gb|BQ040961.1|BQ040961
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAAAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162200888|gb|FC377083.1|FC377083
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|19781146|gb|BQ039660.1|BQ039660
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162199841|gb|FC376707.1|FC376707
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|37824109|gb|BJ582175.1|BJ582175
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|67726367|gb|BJ976626.1|BJ976626
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162204915|gb|FC380597.1|FC380597
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|19786736|gb|BQ040532.1|BQ040532
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162239228|gb|FC416497.1|FC416497
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162214855|gb|FC390990.1|FC390990
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|67508621|gb|BJ941483.1|BJ941483
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162200860|gb|FC377055.1|FC377055
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|67717860|gb|BJ968119.1|BJ968119
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162246164|gb|FC423600.1|FC423600
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|7047316|gb|AW477210.1|AW477210
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162274330|gb|FC450298.1|FC450298
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162200092|gb|FC376554.1|FC376554
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162204916|gb|FC380598.1|FC380598
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|7207529|gb|AW561528.1|AW561528
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162218915|gb|FC394861.1|FC394861
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162214237|gb|FC390283.1|FC390283
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|18340129|gb|BJ172157.1|BJ172157
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162219483|gb|FC396961.1|FC396961
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162276832|gb|FC452514.1|FC452514
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|7207470|gb|AW561471.1|AW561471
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
EST: gi|162236411|gb|FC412778.1|FC412778
EST:     CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG                         CCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT
genomic: CTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTT

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: 34 (upstream exon), 35 (downstream exon)
Score: 54

ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTGgtatgtgttg ... atttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTTTCAAGAAGATTTACGGTGGCCGTAAGAGCAATGGAGTTAGACCGTCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgccgtacgggcttgaaactcattgctccattaattgcctgatttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTTTCAAGAAGATTTACGGTGGCCGTAAGAGCAATGGAGTTAGACCGTCTCA
                                              tttct  CT-rich tract
                                 attaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcatggttaatgcatcgggtttgttctcttacctgtacattgttattgccgtacgggcttgaaactcattgctccattaattgcctgatttctgaagCCTCTATGGCGAGAAAGATCTACCTGAGGGGAGGAATTGGAGTGGGCGCTTTCAAGAAGATTTACGGTGGCCGTAAGAGCAATGGAGTTAGACCGTCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - -ctgtaca