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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatcttcttccttctgttaactgtcgcgctgttttaacattgtacgaccattaatttgaatgtacatagtccgtcagatttattcgccagtacattaaagatagatcttctgacacaggttactcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAGAAACGGAATGGCGTCCAAAATGGTCGTTACTTCATCAACTAAACTATTG

Basic information

species Physcomitrella patens
transcript PP1S47_110V6.1
intron # 11
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|67724271|gb|BJ974530.1|BJ974530
EST:     CATTCCCAAGTTCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAG                         GTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
genomic: CATTCCCAAG-TCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
EST: gi|37821037|gb|BJ579103.1|BJ579103
EST:     CATTCCCAAGTCAACTAAGGCCCGCCCTTTCGCTTCGGGAACNTTCAGAG                         GTAATGGAATTTCTGCGACGCCTTTGTGCAGTGG--AAAACGTGGATCAGA
genomic: CATTCCCAAGTCAACTAAGG-CCGCCCTTTCGCTTCGGGAACCTTCAGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCC-TTGTGCAGTGGAAAAAACGTGGATCAGA
EST: gi|37840353|gb|BJ598361.1|BJ598361
EST:     TAAGGCCGCCCTTTCGCTTCGGGANCNTTCAGAG                         GTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
genomic: TAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
EST: gi|100438589|gb|BY980033.1|BY980033
EST:     CCATTCCCAAGTCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAG                         GTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
genomic: CCATTCCCAAGTCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAG
EST: gi|100410934|gb|BY956255.1|BY956255
EST:     ATTCCCAAGTCAACTAAGGCCGCCCTTTCGCTTCGGGAAACTTCNNAGAG                         -TA-TGGAATTTCTGCGACGCCTTGTGCAGTG-AAAAAACGTGGATCAGA
genomic: ATTCCCAAGTCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTC--AGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGA

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: 21 (upstream exon), 31 (downstream exon)
Score: 7

TTATTGAATGGTATGAAGCATGGTTGCAGCATATTGGTGTCATCCATTCCCAAGTCAACTAAGGCCGCCCTTTCGCTTCGGGAACCTTCAGAGgtactatctt ... actcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAGAAACGGAATGGCGTCCAAAATGGTCGTTACTTCATCAACTAAACTATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttattcgccagtacattaaagatagatcttctgacacaggttactcctgcagGTAATGGAATTTCTGCGACGCCTTGTGCAGTGGAAAAAACGTGGATCAGAGAAACGGAATGGCGTCCAAAATGGTCGTTACTTCATCAACTAAACTATTG
                               ttctgac  putative branch site (score: 7)
                                           ttactcct  putative PPT
                 attaaagata  TA-rich tract