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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcggtcattgaatgctgttgcaatcggcatcaggttggtcggtagtatcgacaacgactcccttaacctatcgatttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACCCCTCGTCGGCCCCGTAAACTACAAGCTCCCGGTTCAGTCTGTGTCAGCG

Basic information

species Physcomitrella patens
transcript PP1S5_176V6.1
intron # 3
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|162264617|gb|FC440900.1|FC440900
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|208374775|gb|DC932044.1|DC932044
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162250920|gb|FC425742.1|FC425742
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162151884|gb|FC328130.1|FC328130
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|100402500|gb|BY954867.1|BY954867
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|208384180|gb|DC911288.1|DC911288
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|162260735|gb|FC435387.1|FC435387
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACC
EST: gi|100385223|gb|BY950815.1|BY950815
EST:     TCAACTCCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGCCATTC-AGCTTTCTACGGC-ATAAGAAAAC
genomic: TCAACTCC-ATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATA-GCACAC
EST: gi|67717986|gb|BJ968245.1|BJ968245
EST:     TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAG                         TTACTCGACGATCGCGTGGGGCCATTCCAGCTTCCTACGGCCATAGCAC
genomic: TTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGG-CCATTCCAGCTTCCTACGGCCATAGCAC

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: 31 (upstream exon), 35 (downstream exon)
Score: 10

GGATCGCAATCTTCTCGTCAGTGCATTTCGTTCTGGCGCAGTTGCCGAACTTCAACTCCATTGCCGGGGTCTCCTTGGCTGCCGCTATCATGTCCTTGAGgtaattcggt ... ttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACCCCTCGTCGGCCCCGTAAACTACAAGCTCCCGGTTCAGTCTGTGTCAGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggttggtcggtagtatcgacaacgactcccttaacctatcgatttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACCCCTCGTCGGCCCCGTAAACTACAAGCTCCCGGTTCAGTCTGTGTCAGCG
                              ccttaac  putative branch site (score: 10)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcggtcattgaatgctgttgcaatcggcatcaggttggtcggtagtatcgacaacgactcccttaacctatcgatttgtgtgcagTTACTCGACGATCGCGTGGGCCATTCCAGCTTCCTACGGCCATAGCACACCCCTCGTCGGCCCCGTAAACTACAAGCTCCCGGTTCAGTCTGTGTCAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT