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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCCTGATTTGGAGCCTCTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgttgcattcagtacccatggaagagtcgttggaggccgtctgtccgtcggaaatataattgatccattgcactgtaatgagtgtgtgtatct...

Basic information

species Physcomitrella patens
transcript PP1S215_25V6.1
intron # 3
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|208376363|gb|DC932273.1|DC932273
EST:     CTGTTGGACGAGGTGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|18356615|gb|BJ188674.1|BJ188674
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|208345629|gb|DC909299.1|DC909299
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|162259779|gb|FC436759.1|FC436759
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|18343486|gb|BJ175524.1|BJ175524
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|18357148|gb|BJ189207.1|BJ189207
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|208371667|gb|DC932496.1|DC932496
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|162259765|gb|FC436758.1|FC436758
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|162221749|gb|FC397081.1|FC397081
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|67578005|gb|BJ950172.1|BJ950172
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|208365150|gb|DC946779.1|DC946779
EST:     CTGTTGGACGAGGTGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|22492644|gb|BU052567.1|BU052567
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|67570549|gb|BJ943373.1|BJ943373
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|208354986|gb|DC914250.1|DC914250
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|208382460|gb|DC927994.1|DC927994
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|18350245|gb|BJ182296.1|BJ182296
EST:     CTGTTGGACGAGACGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|67693833|gb|BJ954066.1|BJ954066
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|18332428|gb|BJ164441.1|BJ164441
EST:     CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAA-CAATGTCCCACTGTTCTTTAA
genomic: CTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA
EST: gi|162221748|gb|FC397080.1|FC397080
EST:     TAGTTGCGAAGTG                         CCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTNTAA
genomic: TAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAA

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), 35 (downstream exon)
Score: 8

TATCCTGATTTGGAGCCTCTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgt ... ggttggccagCCAGAACCATATCAACTTGGTCGTCGTAAACAATGTCCCACTGTTCTTTAATGTGCGGGATGGGCCTTATATGCCTACCCTACGACTTTTGCACCAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCCTGATTTGGAGCCTCTGTTGGACGAGATGCTACCGAAGAAATCGCCACTCATAGTTGCGAAGTGgtgagtatgttgcattcagtacccatggaagagtcgttggaggccgtctgtccgtcggaaatataattgatccattgcactgtaatgagtgtgtgtatct

- - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAA