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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacctgtttacattcgctgcttcagttacgattctgtttaaagaagcgcttcagacatagtagaatattctgatctgtcaagtttttgtaggttttatatctgcatgaaagcctttataattgacagagatatttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGCATGTATCTTCAAGATCTCTTACCAAAGCTCACCGTACCAGACGATGATG

Basic information

species Physcomitrella patens
transcript PP1S47_23V6.2
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|208382438|gb|DC927972.1|DC927972
EST:     TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|100399470|gb|BY972735.1|BY972735
EST:     TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|162223996|gb|FC400354.1|FC400354
EST:     TACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|208352569|gb|DC918278.1|DC918278
EST:     TCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACCAATCTATATGGAGC
genomic: TCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|208398077|gb|DC904382.1|DC904382
EST:     TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|208354231|gb|DC957437.1|DC957437
EST:     CTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: CTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|162223997|gb|FC400355.1|FC400355
EST:     TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
EST: gi|100351812|gb|BY964562.1|BY964562
EST:     CCTGAGGACTTATCTCAACCTATTTTTACCCAGCCTTTCCAAAGTCCAGA                         GTCCTGCACCCCAGCAGC
genomic: CCTGAGGACTTATCTCAACCTATTTT-ACCCAGCCTT-CCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCC-AGCAGC
EST: gi|100409507|gb|BY955967.1|BY955967
EST:     TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACTTTAACAAATCTATATGGGAG
genomic: TTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGG-AG
EST: gi|208351995|gb|DC925804.1|DC925804
EST:     TACCCAG-CTTCCAAAGTCCAGA                         GTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC
genomic: TACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGC

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: 30 (upstream exon), 20 (downstream exon)
Score: 2

GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGAgtaagaacct ... atttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGCATGTATCTTCAAGATCTCTTACCAAAGCTCACCGTACCAGACGATGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaggttttatatctgcatgaaagcctttataattgacagagatatttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGCATGTATCTTCAAGATCTCTTACCAAAGCTCACCGTACCAGACGATGATG
                                aattgac  putative branch site (score: 2)
                                            tatttct  putative PPT
                           tttataattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacctgtttacattcgctgcttcagttacgattctgtttaaagaagcgcttcagacatagtagaatattctgatctgtcaagtttttgtaggttttatatctgcatgaaagcctttataattgacagagatatttctgcagGTCCTGCACCCAGCAGCAGAGAAAATCAACATTAACAAATCTATATGGAGCATGTATCTTCAAGATCTCTTACCAAAGCTCACCGTACCAGACGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA