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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATGCTCCAGCATTTAAGAAAGCGCCCGGAGGCGCACCTGCGAATGTTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatctgctttctggtgggtttgaaatgtcatcataattgtctcaaagcttatgaagatacctcgagttttttcaacctttttacatggatgaaa...

Basic information

species Physcomitrella patens
transcript PP1S127_105V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S127_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ35554 (Selaginella moellendorffii), 5'ss of exon 2
TGCTGATGCTCCAGCATTTAAGAAAGCGCCCGGAGGCGCACCTGCGAATGTTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatctgctttctggtgggtttgaaatgtcatcataattgtctcaaagcttatgaagatacctcgagttttttcaacctttttacatggatgaaa
 |||||||||||||| ||||||||||| || ||||| || || || |||||||||  ||||||  |   ||| | ||||||  | || || || || || ||     ||||  | | || |    ||     |   ||| |       ||||  ||   ||| |   | |    || || |||  ||| | |  |  |  
GGCTGATGCTCCAGCGTTTAAGAAAGCTCCTGGAGGAGCTCCAGCCAATGTTGCTGTTGGTATCTCTCGGCTGGATGGAAACTCTGCTTTCATCGGTAAGgtg-acaatctaatctatgatcaccttttccagctttcaaa-------caaaattttctaagttttttgg----ttctccaccactttgcttttaccag-
















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|100359641|gb|BY947079.1|BY947079
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|67508040|gb|BJ940913.1|BJ940913
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|100368415|gb|BY966999.1|BY966999
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|100404763|gb|BY991271.1|BY991271
EST:     TTGCTTGTGGTATAGCCNAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|100381192|gb|BY950021.1|BY950021
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|162163345|gb|FC339671.1|FC339671
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|18327207|gb|BJ159209.1|BJ159209
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|208353818|gb|DC906506.1|DC906506
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|19789050|gb|BQ041062.1|BQ041062
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACTACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|208360000|gb|DC934917.1|DC934917
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACA-T
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|18371173|gb|BJ202775.1|BJ202775
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|18325903|gb|BJ157901.1|BJ157901
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
EST: gi|100416897|gb|BY993143.1|BY993143
EST:     TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAA                         GTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT
genomic: TTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAAT

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: 23 (upstream exon), 31 (downstream exon)
Score: 12

TGCTGATGCTCCAGCATTTAAGAAAGCGCCCGGAGGCGCACCTGCGAATGTTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatc ... cattccgtagGTTGGCGACGACGAATTTGGGCACATGCTGTGCGACGTTCTGAAGGACAATCATGTGATAACTAATGGTGTTCGGTTCGACTCTCATGCAAGAACGGCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGATGCTCCAGCATTTAAGAAAGCGCCCGGAGGCGCACCTGCGAATGTTGCTTGTGGTATAGCCAAGCTTGGTGGAAAGGCAGCATTTATTGGAAAAgtatgtcatctgctttctggtgggtttgaaatgtcatcataattgtctcaaagcttatgaagatacctcgagttttttcaacctttttacatggatgaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA