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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatcatcatcttttaatttctctagatatccgagtaatgcgattcctgtgtgagctccgataacagtggtgcccgtgtgtctcttattttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.2
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|162228933|gb|FC404726.1|FC404726
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|15261762|gb|BI437072.1|BI437072
EST:     CGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: CGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162218094|gb|FC394957.1|FC394957
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGNGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|100413810|gb|BY974995.1|BY974995
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162170029|gb|FC345082.1|FC345082
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162254392|gb|FC430527.1|FC430527
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162167529|gb|FC344220.1|FC344220
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTG
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTG
EST: gi|162230556|gb|FC407146.1|FC407146
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162263114|gb|FC439780.1|FC439780
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162256673|gb|FC433191.1|FC433191
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162249688|gb|FC426516.1|FC426516
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162198843|gb|FC372870.1|FC372870
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTG
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTG
EST: gi|100431989|gb|BY978609.1|BY978609
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|7047275|gb|AW477169.1|AW477169
EST:     CGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: CGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162270571|gb|FC446496.1|FC446496
EST:     CAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: CAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162262523|gb|FC439735.1|FC439735
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162185364|gb|FC360938.1|FC360938
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|100413123|gb|BY992598.1|BY992598
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
EST: gi|162273997|gb|FC450344.1|FC450344
EST:     TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGG                         CTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT
genomic: TGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGT

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), 35 (downstream exon)
Score: 47

ATTACCTTTGTTCTCGTGGACCTCGCTGATGAGGAGGTGGCCACTCCCGTTCTGGACTTCTTCGCACTTGACAGCGAGAAGACAAGGgtactttcct ... tttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgtgtgagctccgataacagtggtgcccgtgtgtctcttattttaatgcagCTATTGGGATTTGTAGCTGAGGAGACCAGCGGCAAGTACCTGCACGATGGTGACTTCAGTGTTGACTCACTCAAG
                                            ttttaat  putative branch site (score: 47)
                                     tctcttatttt  CT-rich tract
                                     tctcttattttaat  TA-rich tract