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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatacatgatttcaaatagttccaaagtgtgcaagcaaaatttgatatttatttttgatcacatgaattattaggtcgtctcagcttctgccctg...

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 4
TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaat-tatacatgatttcaaatagttccaaagtgtgcaagcaaaatttgatatttatttttgatcacatgaattattaggtcgtctcagcttctgccctg
 |||  |||||||||||||||||| ||||||||||| |||||||  || ||||| || || || || || |||||||| |||||||  || || | |||||  || | |   || |||||| |  |    |      | ||| ||  ||  ||||| |  |||| |||  | ||||   |   ||   ||||  || |
CTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAGgtaagatacaaacccttccaaatattgtccctttt-----gtaaagttgtatgcttattat-aatcagatgc-tgattaaa-cacttctttttctctccag

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 4
TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatacatga--tttcaaatagttcca-------aagtgtgcaagcaaaatttgatatttatttttgatcacatgaatta-ttaggtcgtctcagctt-ctgccctg----------------------
 ||   ||||||||||||  |||| ||||||||||| || ||||  || ||||| || |||||||| || ||||||||||| ||||  || |||| ||||| ||      |  |||| ||   ||  |        | |||  |||    || ||| ||   |  || |     || |||| |||  ||     | ||   |||| ||                      
CTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGgtgaaagaggtaaataccagccaattttctaaccattttacttgctcgactgt-taagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcag
















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|208351962|gb|DC925771.1|DC925771
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|162212343|gb|FC388071.1|FC388071
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|100398742|gb|BY990493.1|BY990493
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGC-AAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|100362914|gb|BY947592.1|BY947592
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|208371459|gb|DC955795.1|DC955795
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
EST: gi|100381366|gb|BY950092.1|BY950092
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGGTGCATGT-GCCTCTGAGAT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTG-TGCATGTTGCCTCTGAGAT
EST: gi|37826136|gb|BJ584148.1|BJ584148
EST:     AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG                         GATGCTACNNNNNNNNGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT
genomic: AGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATT

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: 32 (upstream exon), 34 (downstream exon)
Score: 19

TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatac ... ctgtctacagGATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGgtaattatacatgatttcaaatagttccaaagtgtgcaagcaaaatttgatatttatttttgatcacatgaattattaggtcgtctcagcttctgccctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaaa