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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttctttttcttggctagcttagtcagaaagcttggccaggtttttactaggcaacatgacctcacaagatggatgttgatctccttattcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTTCCAAATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTAT

Basic information

species Physcomitrella patens
transcript PP1S6_173V6.1
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|208374177|gb|DC945223.1|DC945223
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100380002|gb|BY968797.1|BY968797
EST:     CCAGACATCATATGAAGACAACATTAAGAAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATGGCCACTTAGCTCGAGCATCCCCTCTT
genomic: CCAGACATCATATGAAGACAACATTAAGAAAA-TAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100407592|gb|BY991770.1|BY991770
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67718087|gb|BJ968346.1|BJ968346
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67726582|gb|BJ976841.1|BJ976841
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208346475|gb|DC917428.1|DC917428
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208358290|gb|DC930703.1|DC930703
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208395942|gb|DC915702.1|DC915702
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208370208|gb|DC952030.1|DC952030
EST:     AAATAGCTGACNTTAGCACT                         G-GGGAGGANTCT-GGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: AAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67696865|gb|BJ957098.1|BJ957098
EST:     AGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: AGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67725755|gb|BJ976014.1|BJ976014
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100417696|gb|BY975609.1|BY975609
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208348063|gb|DC905386.1|DC905386
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|162232709|gb|FC408116.1|FC408116
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208357605|gb|DC914019.1|DC914019
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100438460|gb|BY979968.1|BY979968
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100426036|gb|BY977245.1|BY977245
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCAT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCAT
EST: gi|67717239|gb|BJ967498.1|BJ967498
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208393913|gb|DC946123.1|DC946123
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208359104|gb|DC930436.1|DC930436
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCAGCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208393221|gb|DC908044.1|DC908044
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100392440|gb|BY953364.1|BY953364
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208376952|gb|DC911048.1|DC911048
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|162232708|gb|FC408115.1|FC408115
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|37826519|gb|BJ584531.1|BJ584531
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208361490|gb|DC939016.1|DC939016
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208349443|gb|DC921931.1|DC921931
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208373323|gb|DC944966.1|DC944966
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCAGCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67718044|gb|BJ968303.1|BJ968303
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100383740|gb|BY969269.1|BY969269
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|37850883|gb|BJ608891.1|BJ608891
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67573484|gb|BJ946308.1|BJ946308
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100378105|gb|BY949683.1|BY949683
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208371216|gb|DC931620.1|DC931620
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTANCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|67726544|gb|BJ976803.1|BJ976803
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208354207|gb|DC902449.1|DC902449
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|208397369|gb|DC916323.1|DC916323
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTT
EST: gi|100400372|gb|BY954444.1|BY954444
EST:     CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACT                         GTGGAAGGATTCTGGGGCATCTATTGCCACTTTAGCTCGAGCATCCACTCT
genomic: CCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTT-AGCTCGAGCATCCACTCT

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: 35 (upstream exon), 32 (downstream exon)
Score: 26

CACCGGTTTGTGTTTTGGTATACTCGAAGGCAGCCAGGCATTCGGTCCCAGACATCATATGAAGACAACATTAAGAAAATAGCTGACTTTAGCACTgtgagttatt ... tcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTTCCAAATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactaggcaacatgacctcacaagatggatgttgatctccttattcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTTCCAAATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTAT
                                    tctccttattc  CT-rich tract
                                         ttattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttctttttcttggctagcttagtcagaaagcttggccaggtttttactaggcaacatgacctcacaagatggatgttgatctccttattcaatctcagGTGGAAGGATTCTGGGGCATCTATTGCCACTTAGCTCGAGCATCCACTCTTCCAAATCCAACCGACTTACATTTGTTCAAGGAAGGCATTCGTCCGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA