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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctagttggttgatccattattaatttgtattgcatctggcctgatttgttgtggattttattttcatcttctcaatctgcagttgtatacatgtataatatttggtagttcgagttaggaattctatgatttatgtgcgcaatgtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATGCCGGAGAAGT

Basic information

species Physcomitrella patens
transcript PP1S426_34V6.1
intron # 4
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|208369961|gb|DC948084.1|DC948084
EST:     TGATGATTGGACGCAAACCAGNTCNTATGC-TGAAGNTANTTTG                         AGACACTCANGGGGAGAC-TAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: TGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|162217444|gb|FC393120.1|FC393120
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208371545|gb|DC936266.1|DC936266
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208355863|gb|DC930226.1|DC930226
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|18366083|gb|BJ198161.1|BJ198161
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208347818|gb|DC917567.1|DC917567
EST:     GGCTGTTGATGA-TGGACGCAAACAAGTTCCTATGCTTGAAGTTACTNTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|100447366|gb|CJ971665.1|CJ971665
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208367118|gb|DC947824.1|DC947824
EST:     AAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: AAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|100358169|gb|BY965507.1|BY965507
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208392547|gb|DC933947.1|DC933947
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|162236819|gb|FC412562.1|FC412562
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|162160226|gb|FC337123.1|FC337123
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|162217443|gb|FC393119.1|FC393119
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208360526|gb|DC950072.1|DC950072
EST:     GGCTGTTGATGATTGGACGCAAACAAGNTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|37846197|gb|BJ604205.1|BJ604205
EST:     GATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208378639|gb|DC903670.1|DC903670
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208374026|gb|DC944759.1|DC944759
EST:     GGCTGNTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
EST: gi|208390426|gb|DC933683.1|DC933683
EST:     GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTG                         AGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG
genomic: GGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATG

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: 33 (upstream exon), 20 (downstream exon)
Score: 3

ATCCTTTCAATTTGGTAGAGAGAAATATCTTACGCCTTGGCTGTTGATGATTGGACGCAAACAAGTTCCTATGCTTGAAGTTACTCTGgtgagtttct ... gtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATGCCGGAGAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttggtagttcgagttaggaattctatgatttatgtgcgcaatgtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATGCCGGAGAAGT
                                            tgttttt  CT-rich tract
                     aattctatgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttctagttggttgatccattattaatttgtattgcatctggcctgatttgttgtggattttattttcatcttctcaatctgcagttgtatacatgtataatatttggtagttcgagttaggaattctatgatttatgtgcgcaatgtttttgcagAGACACTCAGGGGGAGACTTAGAAGGAGTGACTACAAAAGTTGTACCCATGCCGGAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT