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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttacgaattactatgacgattctcataattcaatcataggctaccccaaagttatgcacagccgatttgcacatgaaattgatttgtatttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTAGAGATAAGGTTCTCACCTTTGTAAGAGAGAAA

Basic information

species Physcomitrella patens
transcript PP1S47_196V6.1
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|100361575|gb|BY984075.1|BY984075
EST:     TGATGCTGCTTCAAAGGCGTTGATGCCAGTGCTACGTCAGGATACAAAAG                         GTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
EST: gi|208383270|gb|DC907244.1|DC907244
EST:     TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG                         GTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
EST: gi|162177459|gb|FC353720.1|FC353720
EST:     TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG                         GTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
EST: gi|100363091|gb|BY984352.1|BY984352
EST:     TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG                         GTTCATTGACAGCTTTATTCAAGCACATTGAG
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAG
EST: gi|162186312|gb|FC361620.1|FC361620
EST:     TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAG                         GTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTA
EST: gi|100359470|gb|BY984270.1|BY984270
EST:     TGATGCTGCTTCAAAGGCGTTGATGCCAGTGCTACGTCAGGATACAAAAG                         GGTCATTGACAGCTTTTAT-CAAGCACATTGAGAATTCAGATGAGAACCTT
genomic: TGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTT-ATTCAAGCACATTGAGAATTCAGATGAGAACCTT

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: 13 (upstream exon), 23 (downstream exon)
Score: 1

AAGAGGTTTTGGAGCGTGATGCTGCTTCAAAGGCGTTGATGTCAGTGCTACGTCAGGATACAAAAGgtgctcatcg ... tttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTAGAGATAAGGTTCTCACCTTTGTAAGAGAGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccaaagttatgcacagccgatttgcacatgaaattgatttgtatttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTAGAGATAAGGTTCTCACCTTTGTAAGAGAGAAA
                                 aattgat  putative branch site (score: 1)
                                           tatttcct  putative PPT
                                aaattgatttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttacgaattactatgacgattctcataattcaatcataggctaccccaaagttatgcacagccgatttgcacatgaaattgatttgtatttcctgcagGTTCATTGACAGCTTTATTCAAGCACATTGAGAATTCAGATGAGAACCTTAGAGATAAGGTTCTCACCTTTGTAAGAGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatga