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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTAGCTGGCCAGCGAAAGTAGAAGCTGCAGACTACCATCCTTTGCCATCTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggcattttctaacatttattagggagaagggatatgattctattgcttaacttgtgcatcaacgtccacgcaaacatcattcggcgcagctca...

Basic information

species Physcomitrella patens
transcript PP1S475_2V6.1
intron # 1
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|100416912|gb|BY993150.1|BY993150
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGANAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|18372909|gb|BJ204511.1|BJ204511
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|67578446|gb|BJ950613.1|BJ950613
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|162171220|gb|FC346378.1|FC346378
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|100447818|gb|CJ972117.1|CJ972117
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|67572167|gb|BJ944991.1|BJ944991
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|100452132|gb|CJ975116.1|CJ975116
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGG
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGG
EST: gi|100363224|gb|BY984419.1|BY984419
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|100372450|gb|BY985605.1|BY985605
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|67507761|gb|BJ940640.1|BJ940640
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|18343889|gb|BJ175927.1|BJ175927
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGAC
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGAC
EST: gi|162165943|gb|FC340968.1|FC340968
EST:     NTAA-CTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATT
genomic: -TAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATT
EST: gi|100445740|gb|CJ970039.1|CJ970039
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|162276055|gb|FC452331.1|FC452331
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|162220129|gb|FC395406.1|FC395406
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|67574046|gb|BJ946870.1|BJ946870
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAA
EST: gi|162222735|gb|FC398989.1|FC398989
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|18348573|gb|BJ180622.1|BJ180622
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|18327560|gb|BJ159563.1|BJ159563
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGA
EST: gi|100447282|gb|CJ971581.1|CJ971581
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGANT-ACCGAA-AAG                         AATCGCTTGACTAT
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTAT
EST: gi|162160798|gb|FC336697.1|FC336697
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|100371055|gb|BY985916.1|BY985916
EST:     CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
genomic: CTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA
EST: gi|100409632|gb|BY956028.1|BY956028
EST:     TAAACTGGTCAGTACGCTGCGTAGNCA-GAGAAACGAATTACCGAAGAAG                         ACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAG-ACAAACGGA
genomic: TAAACTGGTCAGTACGCTGCGTAG-CAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGA

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), 35 (downstream exon)
Score: 23

AAGTAGCTGGCCAGCGAAAGTAGAAGCTGCAGACTACCATCCTTTGCCATCTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggc ... gcttttgtagACTCGCTTGACTATTGCCGATGGCCAAGATGAGCCTGAAAGGACAAACGGAGATATTTTGGTGTTTCCCGACATGGTGAAGTATAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTAGCTGGCCAGCGAAAGTAGAAGCTGCAGACTACCATCCTTTGCCATCTAAACTGGTCAGTACGCTGCGTAGCAAGAGAAACGAATTACCGAAGAAGgtacgcaggcattttctaacatttattagggagaagggatatgattctattgcttaacttgtgcatcaacgtccacgcaaacatcattcggcgcagctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG