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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatccatgtacttcaattatctgtctcatttactcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG

Basic information

species Physcomitrella patens
transcript PP1S149_289V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtatatccatgtacttcaattatctgtctcatttactcgtaatggatttgcatctgcagtt-tgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG
                ||   |    | |     | | | | | || |||||     ||   ||  | |||||     |||| ||  | |  | ||  ||  ||   |||  ||     ||||||||||||| |||||||  || ||    |||||||| ||  | || || ||||||||||| ||||||||||||||||| || ||||||||||| || |
---------------acacacaatgatgttgagaa-tggaagttgaattgcactgctaggagtggtgccctgaagttatatt-ttgacctgtatatgcatcatgacctttccta----cagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
------------gtatatccatgtacttcaattatctgtctcatttactcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG
               | |  ||||     |||      |  ||| |       ||   ||| |   || | |       ||||  ||  |  |   || | |||  |||    ||    |   |  | |||||| || |||||||| ||||  || ||    |||||||| ||  | || || |||||| |||| || ||||||||||||||||| ||||||||||| || |
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctt--tcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatatccatgtacttcaattatctgtctcatttac-tcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG
                            |  |  |  |  |||||  || | |     ||  | ||   | |  | ||| | | | || |||  ||   || |||   |   |   | ||||| |||||||| |||||||  || ||    |||||||||||| | || || ||||| ||||| ||||||||||| || ||||| ||||||||| | || |
--------------------------gttagtccatgttataatgttttgggagtcttagaat-catagcagcctggttgtaagtgtc-ttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG

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|208356851|gb|DC926862.1|DC926862
EST:     ANCTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162175003|gb|FC350902.1|FC350902
EST:     AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162156171|gb|FC332546.1|FC332546
EST:     AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACTAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162198559|gb|FC373405.1|FC373405
EST:     AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162192963|gb|FC371946.1|FC371946
EST:     AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162268426|gb|FC444195.1|FC444195
EST:     AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|208369434|gb|DC955895.1|DC955895
EST:     TGTCANGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: TGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
EST: gi|162268425|gb|FC444194.1|FC444194
EST:     AAATTGTCAGGTGGTGTAGCGGTACTTAAG                         ATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT
genomic: AAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACT

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: 16 (upstream exon), 20 (downstream exon)
Score: 1

ATCCGAGAGGCTATCAGCGCTGCCACTTCCGACTACGATAAGGAGAAACTGCAAGAGAGGTTGGCTAAATTGTCAGGTGGTGTAGCGGTACTTAAGgtatatccat ... ataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG
                                       ttttttat  CT-rich tract
                       ttgaaattgattttgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatccatgtacttcaattatctgtctcatttactcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG