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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcaatgcctcctcgattgctgtacttgtttcttgccatgaagacatgtatctttcaggcaacccttacacttcctctaaaagtcctgacttggtttcggtgcggtgtctggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG

Basic information

species Physcomitrella patens
transcript PP1S6_173V6.1
intron # 3
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|208374177|gb|DC945223.1|DC945223
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100407592|gb|BY991770.1|BY991770
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTTAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67718087|gb|BJ968346.1|BJ968346
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATCATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67726582|gb|BJ976841.1|BJ976841
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATCATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208346475|gb|DC917428.1|DC917428
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208358290|gb|DC930703.1|DC930703
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         NATGCTGCTAACCGAAGTGGAGGAA-GTGGATTATCCGATTNAAAA-GCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208395942|gb|DC915702.1|DC915702
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208370208|gb|DC952030.1|DC952030
EST:     ATCCAACCGACTTACATTTGNTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67696865|gb|BJ957098.1|BJ957098
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67725755|gb|BJ976014.1|BJ976014
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208348063|gb|DC905386.1|DC905386
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAA-GCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|162232709|gb|FC408116.1|FC408116
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208357605|gb|DC914019.1|DC914019
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100438460|gb|BY979968.1|BY979968
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208393913|gb|DC946123.1|DC946123
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208359104|gb|DC930436.1|DC930436
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208393221|gb|DC908044.1|DC908044
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208399428|gb|DC924858.1|DC924858
EST:     TTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: TTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100392440|gb|BY953364.1|BY953364
EST:     ATCCAACCGACTTACATTTGTTCNAGGAAAGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208376952|gb|DC911048.1|DC911048
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAA-GCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|162232708|gb|FC408115.1|FC408115
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|37826519|gb|BJ584531.1|BJ584531
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208349443|gb|DC921931.1|DC921931
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208373323|gb|DC944966.1|DC944966
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|37846680|gb|BJ604688.1|BJ604688
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67718044|gb|BJ968303.1|BJ968303
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100383740|gb|BY969269.1|BY969269
EST:     TCCAACCGACTTACATTTTGT-CAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCCGAAGTGGAG-AAAGTGGATTATCCGATTTA
genomic: TCCAACCGACTTACATTT-GTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACC-GAAGTGGAGGAAAGTGGATTATCCGATTTA
EST: gi|37826548|gb|BJ584560.1|BJ584560
EST:     AACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: AACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|37850883|gb|BJ608891.1|BJ608891
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67573484|gb|BJ946308.1|BJ946308
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100378105|gb|BY949683.1|BY949683
EST:     TCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCCGT-ATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: TCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCC-GTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208371216|gb|DC931620.1|DC931620
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         NATGCTGCTAACCGAAGTGGANGAAAGTGGATTATCCGATTTAAAA-GCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|67726544|gb|BJ976803.1|BJ976803
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208354207|gb|DC902449.1|DC902449
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTA-CCGAAGTGGANGAAAGTGGATTATCCGATTTAAAA-GCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208397369|gb|DC916323.1|DC916323
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|100400372|gb|BY954444.1|BY954444
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
EST: gi|208382280|gb|DC919268.1|DC919268
EST:     ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAA                         GATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA
genomic: ATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTA

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: 32 (upstream exon), 22 (downstream exon)
Score: 15

AGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTTCCAAATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTATGGGAAgtaagtttca ... tggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacacttcctctaaaagtcctgacttggtttcggtgcggtgtctggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG
                   tcctgac  putative branch site (score: 15)
                                                aaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcaatgcctcctcgattgctgtacttgtttcttgccatgaagacatgtatctttcaggcaacccttacacttcctctaaaagtcctgacttggtttcggtgcggtgtctggaaaaaagGATGCTGCTAACCGAAGTGGAGGAAAGTGGATTATCCGATTTAAAAAGCTAGTGTCTGGTCGATACTGGGAGGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA