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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtagccaagtctctcttcattaggaacattcattcatacgcgcagttggttccgcaaatattgttctcgttataatttgacctcgtttttcgatgctctgtatattcagtacacatggtacttaccttattgttggatgccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAGAATAGGAGTATTCGAGATTTTCACTCTGCCTTCCTAG

Basic information

species Physcomitrella patens
transcript PP1S4_56V6.1
intron # 2
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|162274342|gb|FC450310.1|FC450310
EST:     ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGG                         GTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
genomic: ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
EST: gi|100378508|gb|BY968634.1|BY968634
EST:     ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGG                         GGTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
genomic: ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
EST: gi|100385363|gb|BY950955.1|BY950955
EST:     ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGAAGTGTTGGG                         GGTGTTGCTGTGGTCCTGCCATCCCTCATTTTTCGT-GTCCTTTTTCATCA
genomic: ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTT-CGTTGTCCTTTT-CATCA
EST: gi|162268064|gb|FC443534.1|FC443534
EST:     ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGG                         GTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
genomic: ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAG
EST: gi|100431017|gb|BY959985.1|BY959985
EST:     ATCTGCGGTACCCCAGGAAGC-AGAGACTGTCCCGACATGGAGTGTTGGG                         GTTGTTGCTGTGGTCC
genomic: ATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCC

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: 33 (upstream exon), 35 (downstream exon)
Score: 18

CTTCATCATTCCACCGTTCCATCGTTTTGTGAATGAACCCATGATGGAAGATCTGCGGTACCCCAGGAAGCCAGAGACTGTCCCGACATGGAGTGTTGGGgtacgtagcc ... gccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAGAATAGGAGTATTCGAGATTTTCACTCTGCCTTCCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgtatattcagtacacatggtacttaccttattgttggatgccttatcagGTTGTTGCTGTGGTCCTGCCATTCCTCATTTTCGTTGTCCTTTTCATCAAGAATAGGAGTATTCGAGATTTTCACTCTGCCTTCCTAG
                         tacttac  putative branch site (score: 18)
                                              ccttatc  putative PPT
     tgtatatt  TA-rich tract