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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctagtgttacaacacccgcttaacgcttcacgagaacttgctaagagaatgacgtacaaaaaatctgtttccatcaggtgtaaacgaatggatcctctaatgtagatggtatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTG

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
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|208370384|gb|DC931796.1|DC931796
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAN                         GTTACTAANACNGTGCCAGCAATGACTGATGCCGTAAAGNACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208379758|gb|DC907643.1|DC907643
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAA-GAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|100359035|gb|BY946813.1|BY946813
EST:     TTCTCAGCGGACTTACCAAG-AAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208394236|gb|DC933904.1|DC933904
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAAAG                         -TTNACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCT-AT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTT-ACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTAT
EST: gi|208363800|gb|DC943257.1|DC943257
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162202525|gb|FC380040.1|FC380040
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|100400200|gb|BY990829.1|BY990829
EST:     TCTCAGCGGACTTACCAAGGAAAGTAAA-GAAGTGGAAAGTGAAGAAGAA                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TCTCAGCGGACTTACCAAGGAA-GTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208372240|gb|DC948043.1|DC948043
EST:     AAAAGNAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: AAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208365324|gb|DC931206.1|DC931206
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|67694015|gb|BJ954248.1|BJ954248
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162149682|gb|FC326733.1|FC326733
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTANAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208389139|gb|DC945715.1|DC945715
EST:     TTCTCAGCGGACTTACCCAGGANGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162163621|gb|FC339531.1|FC339531
EST:     TTCTCAGCGGACTTCCCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208353396|gb|DC946302.1|DC946302
EST:     TCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162238556|gb|FC417411.1|FC417411
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTANAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208386257|gb|DC952970.1|DC952970
EST:     TCAGCGGACNTACCNAGGNAGTAAAAGAAGTNGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|162237619|gb|FC413052.1|FC413052
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|100399885|gb|BY990670.1|BY990670
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCCGTANAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT
EST: gi|208384915|gb|DC903422.1|DC903422
EST:     TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAG                         GTTACTAAGACCGTGCCAGCAATGACTGATGCN-TAAAGGACGCTCTTATT
genomic: TTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATT

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: 51

GCATTCAAGTTGATTGTTACCGACCCAGATTCTGTTCTCAGCGGACTTACCAAGGAAGTAAAAGAAGTGGAAGGTGAAGAAGAGgtgagctagt ... tatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttccatcaggtgtaaacgaatggatcctctaatgtagatggtatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTG
                              ctctaat  putative branch site (score: 51)
                                 taatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctagtgttacaacacccgcttaacgcttcacgagaacttgctaagagaatgacgtacaaaaaatctgtttccatcaggtgtaaacgaatggatcctctaatgtagatggtatgatgtagGTTACTAAGACCGTGCCAGCAATGACTGATGCCGTAAAGGACGCTCTTATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA