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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctcgcgtttttttgcattccctgttcttcttgtcttctgtgagggtgaaacacttcgaatcaggcgagaatgtcgcgaggtttcaatggtgtagaatggacggtttgcttgtttggattgtgatcacttcaagttcttaggttgttgaatttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGACTTTCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATG

Basic information

species Physcomitrella patens
transcript PP1S28_168V6.1
intron # 1
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|100446747|gb|CJ971046.1|CJ971046
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGNAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|208358357|gb|DC934550.1|DC934550
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18347517|gb|BJ179564.1|BJ179564
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18344382|gb|BJ176422.1|BJ176422
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|67508161|gb|BJ941032.1|BJ941032
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18343114|gb|BJ175152.1|BJ175152
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|162159689|gb|FC336075.1|FC336075
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|162189601|gb|FC365823.1|FC365823
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18346124|gb|BJ178167.1|BJ178167
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18351282|gb|BJ183334.1|BJ183334
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18343058|gb|BJ175096.1|BJ175096
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|67572551|gb|BJ945375.1|BJ945375
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|100439543|gb|BY961986.1|BY961986
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|67508549|gb|BJ941412.1|BJ941412
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|162152501|gb|FC328779.1|FC328779
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|162188362|gb|FC364232.1|FC364232
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGA
EST: gi|18373013|gb|BJ204615.1|BJ204615
EST:     CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCG                         AGGTGCGAGCGGGAAGCTGGTAATACTTTACGGTACTGTATTNGCGTGTGA
genomic: CCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGA-GCTGGTAATACTT-ACGGTACTGTATTC-CGTGTGA

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), 23 (downstream exon)
Score: 2

TTTTTGGACACCGTGGGCGGGTTGCGTCTTTGTAAGGCCAACTCTGTTCGCCTCACAGATGTTGGCCTTCCGGTGTCTCTTTCACGGAATCGGAAGCTCGgtgcgctcgc ... atttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGACTTTCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttgtttggattgtgatcacttcaagttcttaggttgttgaatttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGACTTTCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATG
                                         ttgaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctcgcgtttttttgcattccctgttcttcttgtcttctgtgagggtgaaacacttcgaatcaggcgagaatgtcgcgaggtttcaatggtgtagaatggacggtttgcttgtttggattgtgatcacttcaagttcttaggttgttgaatttatgtagAGGTGCGAGCGGGAGCTGGTAATACTTACGGTACTGTATTCCGTGTGACGACTTTCGGGGAGTCACATGGCGGAGGAGTCGGGTGCATTATTGATGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA