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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctacattcagttgctgtctcttggtcatgcttggaattttactcagcatctgccatgaagtactagtccttcaattgataaatgcacaaactacaaatgcttgttgtttttgaaactatgtggtaagctctatctttatgcatcgttggggctgttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGCCGCTAATTTTGCTCACATGTTGGGCTTTAAAGATGAGTTGATGCATGAG

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 10
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|162194038|gb|FC370213.1|FC370213
EST:     TGAATCTGATTGCCCCGCT-GCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGC
genomic: TGAATCTGATTGCCC-GCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGC
EST: gi|162165709|gb|FC340890.1|FC340890
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|208386538|gb|DC952747.1|DC952747
EST:     TGCGTACATATATCNGA-                         GGTGTATAAAGGT-GAGATGTGA-TGCAGCAGA-TCAAGTTTGGATTACGC
genomic: TGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|208373915|gb|DC940426.1|DC940426
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAN                         GGTGTATAA-GGTGGAGATGTGATTGCAGCANATNCANGTTTGGATTACGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|162176173|gb|FC351915.1|FC351915
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGGAT-ACG
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGG-ATTACG
EST: gi|162233299|gb|FC409849.1|FC409849
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|100352729|gb|BY945419.1|BY945419
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGC
EST: gi|19783472|gb|BQ040017.1|BQ040017
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCCAGTTTGGATTAC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTAC
EST: gi|162258522|gb|FC434737.1|FC434737
EST:     ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG                         GGTGTATAAAGGTGGAGATGTGATTGCAGC
genomic: ATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGC

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), 34 (downstream exon)
Score: 32

GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAGgtaagctaca ... ttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGCCGCTAATTTTGCTCACATGTTGGGCTTTAAAGATGAGTTGATGCATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaactatgtggtaagctctatctttatgcatcgttggggctgttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGCCGCTAATTTTGCTCACATGTTGGGCTTTAAAGATGAGTTGATGCATGAG
                                          ctgttttct  CT-rich tract
                     tatctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctacattcagttgctgtctcttggtcatgcttggaattttactcagcatctgccatgaagtactagtccttcaattgataaatgcacaaactacaaatgcttgttgtttttgaaactatgtggtaagctctatctttatgcatcgttggggctgttttctgtagGGTGTATAAAGGTGGAGATGTGATTGCAGCAGATTCAAGTTTGGATTACGCCGCTAATTTTGCTCACATGTTGGGCTTTAAAGATGAGTTGATGCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG