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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggttcacgtgcgtccctcatagctatagcccgagttgggttgcagattgagtagggttggatgcgagctatagggcttattgagagtggttgaggaattggattcgttgcatactgtatattcaaagtggacttagtttgcgtggggtgagtatcacttacggtggcgagggatggcctttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTGTGCGTGCGAGGGCTGAGTGCCGGAAAGGTATTTTCCGACGAAGAGTCAA

Basic information

species Physcomitrella patens
transcript PP1S204_22V6.1
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|18362609|gb|BJ194680.1|BJ194680
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18328336|gb|BJ160340.1|BJ160340
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18359914|gb|BJ191975.1|BJ191975
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18327270|gb|BJ159272.1|BJ159272
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18329206|gb|BJ161212.1|BJ161212
EST:     AGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: AGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18365684|gb|BJ197761.1|BJ197761
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18374970|gb|BJ206548.1|BJ206548
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|100396548|gb|BY990180.1|BY990180
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18368933|gb|BJ201018.1|BJ201018
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18375288|gb|BJ206866.1|BJ206866
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18343567|gb|BJ175605.1|BJ175605
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18329759|gb|BJ161765.1|BJ161765
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
EST: gi|18358397|gb|BJ190456.1|BJ190456
EST:     CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACG                         GAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG
genomic: CTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTG

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), 34 (downstream exon)
Score: 9

CTTGGCAGCAAAGGTTTGCTCTTGGTTGCGATTCCACACTGTTTCTGGCGCTCAGGGGTAGGGAGCGAGTTCTGCTGCCACCGAGCAAGGATCTTTCACGgtgagttggt ... tttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTGTGCGTGCGAGGGCTGAGTGCCGGAAAGGTATTTTCCGACGAAGAGTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttgcgtggggtgagtatcacttacggtggcgagggatggcctttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTGTGCGTGCGAGGGCTGAGTGCCGGAAAGGTATTTTCCGACGAAGAGTCAA
                     cacttac  putative branch site (score: 9)
                                           ccttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttggttcacgtgcgtccctcatagctatagcccgagttgggttgcagattgagtagggttggatgcgagctatagggcttattgagagtggttgaggaattggattcgttgcatactgtatattcaaagtggacttagtttgcgtggggtgagtatcacttacggtggcgagggatggcctttggggtagGAGCTGGTATATGCGGAGTCCAACAGAAGCTTGTGCAGGACTCTTGAGTTGTGCGTGCGAGGGCTGAGTGCCGGAAAGGTATTTTCCGACGAAGAGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA