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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtctactttactgcttctttcgcatactcctgaaagtcaatttggttaatccacgccacactgcttgtgaagccatctgaaagtcgtgtgcgattcctttgttcctgttcgcccaaaatacgattcaaggatgtcagtgttgaatggtccttgacaaccgtcacatacctcaatctgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCACTTCGTTAGCGATGGCGCTGCTCAAGACTATTTTGTGTCATCATGGGCAG

Basic information

species Physcomitrella patens
transcript PP1S97_287V6.1
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|162200892|gb|FC377087.1|FC377087
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|100365116|gb|BY966818.1|BY966818
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAAGT-GCATCA
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAA-GTTGCATCA
EST: gi|162280434|gb|FC456347.1|FC456347
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|100407039|gb|BY973977.1|BY973977
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACCAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|67709712|gb|BJ965528.1|BJ965528
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCGG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|162155583|gb|FC331534.1|FC331534
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|162220086|gb|FC397031.1|FC397031
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|100395338|gb|BY953687.1|BY953687
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|162265304|gb|FC440422.1|FC440422
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
EST: gi|162267601|gb|FC444664.1|FC444664
EST:     CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAG                         TTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC
genomic: CTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCAC

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: 8 (upstream exon), 34 (downstream exon)
Score: 3

TAGGGATACGTTTCAGCCGAGTCCGTTGTGGAAATCACTTGCGCCTGACCCTAACGCAATTGATCAAGGACCTACAGAGAAACCTCTTCTCTTTACGCAGgtggtctact ... tgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCACTTCGTTAGCGATGGCGCTGCTCAAGACTATTTTGTGTCATCATGGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcagtgttgaatggtccttgacaaccgtcacatacctcaatctgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCACTTCGTTAGCGATGGCGCTGCTCAAGACTATTTTGTGTCATCATGGGCAG
                                          atctgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtctactttactgcttctttcgcatactcctgaaagtcaatttggttaatccacgccacactgcttgtgaagccatctgaaagtcgtgtgcgattcctttgttcctgttcgcccaaaatacgattcaaggatgtcagtgttgaatggtccttgacaaccgtcacatacctcaatctgattgccagTTGACAAGGTTAGCTGGTGGAGGAGTGGTGTTAGCAGTCAAGTTGCATCACTTCGTTAGCGATGGCGCTGCTCAAGACTATTTTGTGTCATCATGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT