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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtacatgtaaacagtaaaacatcaggaagggtagctttttgtactcctgttcacgtggtatagtctaccattttctcgccgttttatttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCTTGTCGTAGTGT

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ13606 (Selaginella moellendorffii), 3'ss of exon 1
tttgtacatgtaaacagtaaaacatcaggaagggta--gctttttgtactcctgttcacgtggtatagtctaccattttctcgccgttttatttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCTTGTCGTAGTGT
   |     | |||  |       | || |  |||   | | ||| |  |  | ||  | |  | |  |    ||||| ||   | |  | ||||||||||||| || ||| | || ||||| |||||||| || ||||||||||||||||||||||| |||||
cccgagagaggaaagcgagctcttttagtattggttttgttctttctttttttcttttctttctttttttctgcatttcctt-tcatcgt-tttttttgcagATTGAGCCAATTCCAAGTGGAAATCTGCCACCAGGGTTTGATGCAACTTCTTGTCGCAGTGT
















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|100356992|gb|BY983639.1|BY983639
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCGACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|18361063|gb|BJ193127.1|BJ193127
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|208376147|gb|DC910999.1|DC910999
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|18342648|gb|BJ174683.1|BJ174683
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|162258161|gb|FC433943.1|FC433943
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|100420202|gb|BY975968.1|BY975968
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|208368756|gb|DC940051.1|DC940051
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|100450649|gb|CJ974369.1|CJ974369
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|162254430|gb|FC430656.1|FC430656
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|208391587|gb|DC933836.1|DC933836
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|18326916|gb|BJ158916.1|BJ158916
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|100409806|gb|BY956113.1|BY956113
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
EST: gi|162152881|gb|FC328975.1|FC328975
EST:     CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAG                         ATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT
genomic: CACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCT

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: 28 (upstream exon), 35 (downstream exon)
Score: 8

AAAACATCAAAGTCTCGTGCAAGTTATGCTGCAGCAGAATCAGCATCAACCACAGCAGCAAGCGCTTTATCACCCTGGCTTGCTTGCCACAATACCCCAGgtactccaac ... ttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCTTGTCGTAGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcctgttcacgtggtatagtctaccattttctcgccgttttatttttttgcagATGGAACCATTGCCGAGTGGGAATCTGCCCCCTGGGTTTGATGCAACTTCTTGTCGTAGTGT
                            ttttctcgccgtttta  CT-rich tract
                                       ttttatttttttgca  TA-rich tract