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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGATCATTCCGACTGGACTATGTCTCAATGTGCTACTGCAGCCTATACATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacgattccttctgtgttggctacgaatgttggctatgaaaaaaccacagttacacttgcgaagagattcgctgtttcctgcctatcacaatactcaaagccttgtaaacggtaattctgtag

Basic information

species Physcomitrella patens
transcript PP1S98_36V6.1
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|208398476|gb|DC924746.1|DC924746
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208346548|gb|DC916814.1|DC916814
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208366308|gb|DC943840.1|DC943840
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208363377|gb|DC946975.1|DC946975
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCAAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208347378|gb|DC925346.1|DC925346
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208370716|gb|DC948253.1|DC948253
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|67698630|gb|BJ958863.1|BJ958863
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208365541|gb|DC954782.1|DC954782
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208368267|gb|DC951519.1|DC951519
EST:     ATNTACACTTAANGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGGTATGAAACGGGGNCACCGAGCGATCCAAATTTTACGAAACTTTGGC
genomic: ATCTACACTTAA-GAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTAC-CCGAGCGATCCAAATTTTACGAAACTTTGGC
EST: gi|208392853|gb|DC928539.1|DC928539
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208345900|gb|DC921085.1|DC921085
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208373612|gb|DC952437.1|DC952437
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCGAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208393705|gb|DC946055.1|DC946055
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208367982|gb|DC951007.1|DC951007
EST:     CATCTACACTTAAGAAATTTCANGGANGGATCGCAAGTNCCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208353455|gb|DC946319.1|DC946319
EST:     CATCTACACTTAAGAAATACCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208377562|gb|DC922665.1|DC922665
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
EST: gi|208371846|gb|DC951838.1|DC951838
EST:     CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACG                         GTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT
genomic: CATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCT

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: 14 (upstream exon), 22 (downstream exon)
Score: 1

GAATGATCATTCCGACTGGACTATGTCTCAATGTGCTACTGCAGCCTATACATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacg ... aattctgtagGTTGCTATGAAACTGGTACCCGAGCGATCCAAATTTTACGAAACTTTGGCTCTTGGCAACTCTACTGCGGATATGGAGCGATTTGTTACTGAGTTCTCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGATCATTCCGACTGGACTATGTCTCAATGTGCTACTGCAGCCTATACATCTACACTTAAGAAATATCATGGATGGATTGCAAGTACCGCATTCACGgtatgtgacgattccttctgtgttggctacgaatgttggctatgaaaaaaccacagttacacttgcgaagagattcgctgtttcctgcctatcacaatactcaaagccttgtaaacggtaattctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA