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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctttctactgtcaggtgtttcattcagacgttcaaagtacctgcatttagtacggttccttgcagttcctagcttgtatttgattcttcggtc...

Basic information

species Physcomitrella patens
transcript PP1S46_63V6.3
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_63V6.4 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA17G03700.1 (Glycine max), 5'ss of exon 14
CTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtag-gctctttctactgtcaggtgtt---tcattcagacgttcaaagtacctgcatttagtacggttccttgcagttcctagcttgtatttgattcttcggtc--
                              |  |  | ||||| | |||||| ||||| |||||||||||||| ||||||||||| ||||| || ||||||||| |     | |    |||  |  |   | |||   |  ||     |       |||  |       ||  | ||    ||||||  |||| |   |   |   
-----------------------------AGTCTTACACCTTATGAATTTGTTGAAAGTATGAAGAAGAAGGGCATCCGTGTTCCAGGAATAGGGCACAGgtagtgtatactgtgtgttcatatactaatttattactattttgtttttgttgttgtttcttttaaaatctaactgtatgaagcttggttttgttctgtaaattag

upper sequence: PP1S46_63V6.4 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA07G36840.1 (Glycine max), 5'ss of exon 16
CTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctttctactgtcaggtgtttcattcagacgttcaaagtacct-gcatttagtacggttccttgcagttcctagcttgtatttgatt---cttcggtc----------
                              |  |  ||||||| | |||||| ||||| |||||||| ||||| ||||||||||| ||||| || |||||||||    | | ||||||   |||||   ||   |  ||  || ||  | |  |||  |   ||| |||  |    |||  ||||||  |  |    || | ||          
-----------------------------AGTCTTACGCCTTATGAATTTGTTGAAAGTATGAAGAATAAGGGCATCCGTGTTCCAGGAATAGGGCACAGgtag----tgtatactgt---gtgttcatttactaaattataactattttgtttttgttgttgtttcttttaaaatctaa-ttgtatgaggcttgattttgttctgtaaattag

upper sequence: PP1S46_63V6.4 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT3G06650.1 (Arabidopsis thaliana), 5'ss of exon 15
CTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctc-----------------tttctactgtcaggtgtttcattcagacgttcaaagtacc----tgcatttagtacggttccttgcagttcctagcttgtatttg--attcttcggtc--------------------------
                                 |  | ||||| | ||| |||||| ||||||||||||| || |||||||| ||||| ||||| |||||||| |  |                 | |  |  ||  | | |  |||  | | ||  ||| |  |    |  ||  |  | |  |||||    |   ||||  | |      |||||  |                             
-----------------------------AATCTCACACCTTATGAATTCGTGGAAGGCATGAAGAAGAAAGGAATCCGTGTCCCTGGCATTGGTCACAGgtaagaacaaacaaacgagcttagatcttcatcgtttgttttcacatgtaaatgtggaaattggcgttatatatcaatcaagtatcctttttatcaatagcaggaacagaacattctctgactggatttgttttcttacatatttgtag

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|208366526|gb|DC955602.1|DC955602
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|100385297|gb|BY950889.1|BY950889
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGC-ACAG                         GATCAGGAGTCGAGATAAC
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctttctactgtcaggtgtttcattcagacgttcaaagtacctgcatttagtacggttccttgcagttcctagcttgtatttgattcttcggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG