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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGACAAAGAGAATGATGAGAAGAATCGGCGTGTTCGAGAAGGTGATGATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttggtctgcagtatccctctttcgacatttgtggaatttgaaaccctaattccttcgcacttcttcgtgagtttgcgatgctggttttgaacca...

Basic information

species Physcomitrella patens
transcript PP1S6_173V6.1
intron # 1
splice site 5'
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:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100380002|gb|BY968797.1|BY968797
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTAACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100407592|gb|BY991770.1|BY991770
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67718087|gb|BJ968346.1|BJ968346
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208346475|gb|DC917428.1|DC917428
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208358290|gb|DC930703.1|DC930703
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208395942|gb|DC915702.1|DC915702
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67725755|gb|BJ976014.1|BJ976014
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100417696|gb|BY975609.1|BY975609
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208348063|gb|DC905386.1|DC905386
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|18347330|gb|BJ179376.1|BJ179376
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGA
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGA
EST: gi|162232709|gb|FC408116.1|FC408116
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208357605|gb|DC914019.1|DC914019
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100438460|gb|BY979968.1|BY979968
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCAAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100426036|gb|BY977245.1|BY977245
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67717239|gb|BJ967498.1|BJ967498
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208393913|gb|DC946123.1|DC946123
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208359104|gb|DC930436.1|DC930436
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208393221|gb|DC908044.1|DC908044
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|18344906|gb|BJ176947.1|BJ176947
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100392440|gb|BY953364.1|BY953364
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208376952|gb|DC911048.1|DC911048
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|37826519|gb|BJ584531.1|BJ584531
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCNTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208361490|gb|DC939016.1|DC939016
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208349443|gb|DC921931.1|DC921931
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67718044|gb|BJ968303.1|BJ968303
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100383740|gb|BY969269.1|BY969269
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67573484|gb|BJ946308.1|BJ946308
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100378105|gb|BY949683.1|BY949683
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208371216|gb|DC931620.1|DC931620
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|67726544|gb|BJ976803.1|BJ976803
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208354207|gb|DC902449.1|DC902449
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|208397369|gb|DC916323.1|DC916323
EST:     TCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: TCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
EST: gi|100400372|gb|BY954444.1|BY954444
EST:     ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAG                         CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG
genomic: ATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 10

GAAGGACAAAGAGAATGATGAGAAGAATCGGCGTGTTCGAGAAGGTGATGATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttgg ... gtgttcacagCACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGACAAAGAGAATGATGAGAAGAATCGGCGTGTTCGAGAAGGTGATGATCGGGACAGACAGACTCGAGAAATTCGAGCTGGCTTACATCCTCTGCAGgtagctttggtctgcagtatccctctttcgacatttgtggaatttgaaaccctaattccttcgcacttcttcgtgagtttgcgatgctggttttgaacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG