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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttccttcacctttacctcttttttctttttcttatccctccaaaatttgaagaaaacggcaatttgaacttaggaacaggactaagtttttgtcctatatctgctgactgctcttctcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGCTGTTTGTCAACGAAGGGGACATGATCCAAGTGGACACGCGAAAAAGCGA

Basic information

species Physcomitrella patens
transcript PP1S49_243V6.1
intron # 6
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|208347503|gb|DC925387.1|DC925387
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208380630|gb|DC919388.1|DC919388
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|7147836|gb|AW509758.1|AW509758
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAATGGAGACACAGCTCAAG                         GATGATCGAAGCCAGCTACAACATAGACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208351044|gb|DC910507.1|DC910507
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTANTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208374301|gb|DC941142.1|DC941142
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTANTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208350709|gb|DC918169.1|DC918169
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208396719|gb|DC924331.1|DC924331
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|100362161|gb|BY947220.1|BY947220
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208348904|gb|DC921676.1|DC921676
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208348263|gb|DC905505.1|DC905505
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTANTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|67696624|gb|BJ956857.1|BJ956857
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208344391|gb|DC912750.1|DC912750
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAATGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208379070|gb|DC911595.1|DC911595
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         NAGAATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAATGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|162221894|gb|FC398162.1|FC398162
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208357149|gb|DC926524.1|DC926524
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|162221893|gb|FC398161.1|FC398161
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208392456|gb|DC904274.1|DC904274
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAATGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
EST: gi|208361708|gb|DC954142.1|DC954142
EST:     TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAG                         GAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC
genomic: TGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGC

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), 35 (downstream exon)
Score: 7

GTTCTTGATGTAGATCTGCCCATCACAGTAGTTGTGAAGGTCGTACAGACGGATCCTGGTTTGAAGGGAGACACAGCTCAAGgttttccttc ... tcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGCTGTTTGTCAACGAAGGGGACATGATCCAAGTGGACACGCGAAAAAGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaacaggactaagtttttgtcctatatctgctgactgctcttctcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGCTGTTTGTCAACGAAGGGGACATGATCCAAGTGGACACGCGAAAAAGCGA
                              tgctgac  putative branch site (score: 7)
                                    ctgctcttctcatt  CT-rich tract
           taagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttccttcacctttacctcttttttctttttcttatccctccaaaatttgaagaaaacggcaatttgaacttaggaacaggactaagtttttgtcctatatctgctgactgctcttctcattaacagGAGGATCGAAGCCAGCTACAACAGAAACAGGTGCCGTAGTGAGCGTGCCGCTGTTTGTCAACGAAGGGGACATGATCCAAGTGGACACGCGAAAAAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA