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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcaggcatgtttcatatggttggttatttgaaagttgcagtttcctgacgtttttgagtctgttttgtgctgacaatttgatttgttttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAACTAGCCAACTTGCCTGAAGAACCAACTGCTGGTCAAACAGGACCTGCAA

Basic information

species Physcomitrella patens
transcript PP1S47_175V6.1
intron # 7
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|208400386|gb|DC925024.1|DC925024
EST:     AAGTCACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208353342|gb|DC946290.1|DC946290
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208363065|gb|DC946934.1|DC946934
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|100379831|gb|BY949966.1|BY949966
EST:     AGTTTACTGA-GAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATAAATTGTAGT
genomic: AGTT-ACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGT
EST: gi|67724008|gb|BJ974267.1|BJ974267
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208366345|gb|DC943863.1|DC943863
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|67692423|gb|BJ952656.1|BJ952656
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208373997|gb|DC944730.1|DC944730
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208354200|gb|DC957420.1|DC957420
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|7286494|gb|AW598981.1|AW598981
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|67725438|gb|BJ975697.1|BJ975697
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208361102|gb|DC957553.1|DC957553
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208368388|gb|DC955557.1|DC955557
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|162275152|gb|FC451739.1|FC451739
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|162272917|gb|FC448853.1|FC448853
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
EST: gi|208368823|gb|DC951347.1|DC951347
EST:     AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT                         TGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA
genomic: AAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAA

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), 21 (downstream exon)
Score: 8

GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATATgtaagttttt ... ttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAACTAGCCAACTTGCCTGAAGAACCAACTGCTGGTCAAACAGGACCTGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgacgtttttgagtctgttttgtgctgacaatttgatttgttttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAACTAGCCAACTTGCCTGAAGAACCAACTGCTGGTCAAACAGGACCTGCAA
                                       tttgtttt  CT-rich tract
                                aatttgatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcaggcatgtttcatatggttggttatttgaaagttgcagtttcctgacgtttttgagtctgttttgtgctgacaatttgatttgttttgtgtgcagTGGATGTACATAGTCCCTTTTGGATTAATTGTAGTGAACGCTCTCAGTCAACTAGCCAACTTGCCTGAAGAACCAACTGCTGGTCAAACAGGACCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC