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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcctccatgccatcaagcgattgtctgcaccttagcggaggtcatcaacgaatattggcaacttcctatgcttaattatttttacatttgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAACACGTCTGATGATCCTCACAAGCGCAAGCCTGACATTTCTAAGGCTAAGG

Basic information

species Physcomitrella patens
transcript PP1S209_52V6.1
intron # 6
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|162196627|gb|FC374917.1|FC374917
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162207029|gb|FC383038.1|FC383038
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162194369|gb|FC371087.1|FC371087
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162194791|gb|FC371638.1|FC371638
EST:     CCTTCAATCTGGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162261552|gb|FC437569.1|FC437569
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|67699664|gb|BJ959897.1|BJ959897
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|37852244|gb|BJ610252.1|BJ610252
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162193738|gb|FC371265.1|FC371265
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162181365|gb|FC358434.1|FC358434
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162196626|gb|FC374916.1|FC374916
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|67695896|gb|BJ956129.1|BJ956129
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162155078|gb|FC330872.1|FC330872
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162245552|gb|FC424106.1|FC424106
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|37825569|gb|BJ583635.1|BJ583635
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162193739|gb|FC371266.1|FC371266
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|18338390|gb|BJ170414.1|BJ170414
EST:     CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
genomic: CCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC
EST: gi|162207028|gb|FC383037.1|FC383037
EST:     AGTTTACCATGCTGGAACTTGCAGAG                         GTGGTTAAGGAGGTGATTGACCTTTTTGCAACAATGGAGTACAAGGAGAAC
genomic: AGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAAC

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: 22

GTGGAGGGACTGATGAGGTTGATGGAAGGTGAACACGTTGGGCCCTTCAATCTCGGAAATCCTGGCGAGTTTACCATGCTGGAACTTGCAGAGgttagcaatt ... tgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAACACGTCTGATGATCCTCACAAGCGCAAGCCTGACATTTCTAAGGCTAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaacgaatattggcaacttcctatgcttaattatttttacatttgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAACACGTCTGATGATCCTCACAAGCGCAAGCCTGACATTTCTAAGGCTAAGG
                          gcttaat  putative branch site (score: 22)
                       tatgcttaattatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcctccatgccatcaagcgattgtctgcaccttagcggaggtcatcaacgaatattggcaacttcctatgcttaattatttttacatttgtgatgcagGTGGTTAAGGAGGTGATTGACCCTTCTGCAACAATCGAGTACAAGGAGAACACGTCTGATGATCCTCACAAGCGCAAGCCTGACATTTCTAAGGCTAAGG

- - - - - - - - - - - - - ctgcacc