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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatctagtctaccgactcaatgttgcagctcgttattcttagtgatctcttttcctttaagcgctcgtacttgtgtagtgtttgactaggaattgaagcacttatccaagtgtttgtgaaattgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTCTCGTGGATTTTGAACTGGGTCATCATATTCCTGGGAGTGCTGCTCATGC

Basic information

species Physcomitrella patens
transcript PP1S5_176V6.1
intron # 5
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|67726489|gb|BJ976748.1|BJ976748
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|208400809|gb|DC925089.1|DC925089
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCNGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|37827465|gb|BJ585477.1|BJ585477
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162273084|gb|FC447778.1|FC447778
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162151795|gb|FC328652.1|FC328652
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162264616|gb|FC440899.1|FC440899
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|67725436|gb|BJ975695.1|BJ975695
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162151883|gb|FC328129.1|FC328129
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162273083|gb|FC447777.1|FC447777
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         TTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162175568|gb|FC351792.1|FC351792
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|208358586|gb|DC946547.1|DC946547
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|15261771|gb|BI437081.1|BI437081
EST:     CTCTTCTTGG-TTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|67726227|gb|BJ976486.1|BJ976486
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162175567|gb|FC351791.1|FC351791
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162224629|gb|FC400525.1|FC400525
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162260734|gb|FC435386.1|FC435386
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162224628|gb|FC400524.1|FC400524
EST:     CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: CTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
EST: gi|162182869|gb|FC358953.1|FC358953
EST:     GGATTCGCCTTCGCTCCTACAACATACTTT                         CTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC
genomic: GGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTC

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: 33 (upstream exon), 34 (downstream exon)
Score: 31

CTTTTACTGCGTTTGTCGGTATGACGTTCCCCTTCTTTGGAGCTCTTCTTGGTTTCTTCGGAGGATTCGCCTTCGCTCCTACAACATACTTTgtaagaatct ... attgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTCTCGTGGATTTTGAACTGGGTCATCATATTCCTGGGAGTGCTGCTCATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtttgactaggaattgaagcacttatccaagtgtttgtgaaattgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTCTCGTGGATTTTGAACTGGGTCATCATATTCCTGGGAGTGCTGCTCATGC
    gtttgac  putative branch site (score: 31)
               aattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatctagtctaccgactcaatgttgcagctcgttattcttagtgatctcttttcctttaagcgctcgtacttgtgtagtgtttgactaggaattgaagcacttatccaagtgtttgtgaaattgtggcagCTGCCGTGTATCATGTGGCTGTGCATCGTCAAGCCCAAGGCATTCAGTTTCTCGTGGATTTTGAACTGGGTCATCATATTCCTGGGAGTGCTGCTCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT