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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttgtatgttctttttgtcgttgaattattcaaatgttacatgaacatgtatcatgtgtacatgtggggcatagggtaaatcttgagtgttgagcttactcttttatcttttgggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA

Basic information

species Physcomitrella patens
transcript PP1S117_137V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 11
gtacacttgtatgttctttttgtcgttgaattattcaaatgttacatgaacatgtatcatgtgtacatgtggggcatagggtaaatcttgagtgttgagcttactcttttatcttttgggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA
                                  ||     | |||||||     ||    |  |  | |    ||   | |||  ||  |     || |  ||||| |  || | |       ||| ||||||||||||||||||||||| ||||||||| | |||||| | ||||| ||||| ||     | 
-------------------------------gtctctctcttaacatgaaatctcattgactcaatttttttcccaatagctaa--ctaaaa----gaacc-actctctcctcctcttt-----cagagTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCG

upper sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacacttgtatgttctttttgtcgttgaattattcaaatgttacatgaacatgtatcatgtgtacatgtggggcatagggtaaatcttgagtgttgagcttactcttttatcttttgggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA
                           | |    ||     | |||||||     ||    |  |  | |    ||   | |||  ||  |     || |  ||||| |  || | |       ||| ||||||||||||||||||||||| ||||||||| | |||||| | ||||| ||||| ||     | 
---------------------------gcaagtctctctcttaacatgaaatctcattgactcaatttttttcccaatagctaa--ctaaaa----gaacc-actctctcctcctcttt-----cagAGTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCG
















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|37837109|gb|BJ595117.1|BJ595117
EST:     GATTAATGCTGCAAAAGACAG                         GGNTTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATT
genomic: GATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGG--TTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATT
EST: gi|208369319|gb|DC955864.1|DC955864
EST:     TAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: TAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|37847718|gb|BJ605726.1|BJ605726
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|162248181|gb|FC422513.1|FC422513
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|18337201|gb|BJ169225.1|BJ169225
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|37828121|gb|BJ586133.1|BJ586133
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|67726258|gb|BJ976517.1|BJ976517
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAATGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|162199120|gb|FC374590.1|FC374590
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|37826062|gb|BJ584074.1|BJ584074
EST:     CCACTTGCCAGACCCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: CCACTTGCCAGA-CCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|162198994|gb|FC374542.1|FC374542
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
EST: gi|162248182|gb|FC422514.1|FC422514
EST:     GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAG                         GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC
genomic: GCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCC

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), 15 (downstream exon)
Score: 7

TGACGGTACTAGTTGCAATTTCCCTTCTTGCTCCTGTAGTTGGCGCAGAAGCCACTTGCCAGACCATGTTGCCTGTGGTGATTAATGCTGCAAAAGACAGgtacacttgt ... gggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcatagggtaaatcttgagtgttgagcttactcttttatcttttgggatgacagGGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA
                         agcttac  putative branch site (score: 7)
                               ctcttttatcttttg  CT-rich tract
                                  ttttatctttt  TA-rich tract