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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC

Basic information

species Physcomitrella patens
transcript PP1S381_39V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                                                                 | |||| || | |    | | |    |||   |||||     |   |    ||   ||| |||         ||  |||| | ||            |||  ||||        || ||| |||||||  || | || || |||||  | ||    || || || ||||||||||| |||| ||||||||||||||| || ||||| ||||| || |||||  
-----------------------------------------------------------------taaatg-actcttctccaaaacaaattgctctcgagtc-acagcatcatataataaagtttgt---------tgtgtttgctgta------------ctacttattttaaacattgtttgcagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttata-taggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                                                                                          |    |  ||| |   ||  |       |    | |    |    ||||||||    | | |  |  |     | |  ||||     |  || ||| |||| ||  || | || || |||||  | ||    || || || || |||||||| |||| ||||||||||||||| || ||||| ||||| || |||||  
-----------------------------------------------------------------------------------------ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgccttaaagtcacaacatttctttaccacttatttcaaatactgtttgcagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacc---tttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                                                                                || ||  | |||       | ||| |   | |  |      | |   ||||||||   |||||| |  | ||  ||   |   |  |   |     | ||    || | |||||||  |||| || || |||||| |||||  ||| ||| | || |||||||||||||  || |||||||||||||| || ||||||||||| |||||  
-------------------------------------------------------------------------------tgtttacttctgt-----taattttttaatgccttgtttattaatagttgtacaccaaatttgccatctgatttcatcact---ctttcttttcccattgt----atggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                                                                                       | |     ||  | ||| || | |  |         | |  || |  |      ||||   | || |  | | | ||   | ||          || | |||| ||  |||| || || |||||  |||||  ||| ||| | || |||||||||||||  || |||||||||||||| || ||||||||||| |||||  
--------------------------------------------------------------------------------------gtttacttctgttaatttttgaatggccttgtttatttata-gttctacaccaaatttgtcatcta-actttatcactctttcttttcccattgtatggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA

upper sequence: PP1S381_39V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ29918 (Selaginella moellendorffii), 3'ss of exon 1
gtaattagggtggcctttttgttgcatgtctttgagccatgcggacttctctgtactgtagaaagtgaatgtacacctacgtatagctgtgtgcgtgcgagtttgtggaggcgcgcaagcgagtgtgtgtacacctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                                                                                                                                |||   | ||   |    ||   |  |        |   || ||          ||  |||||||||| || ||||| |||||| |||| |||||||| || ||||||||||| || |||||| |||| || || || ||||| || || ||||||||  
--------------------------------------------------------------------------------------------------------------------------------gtaagacgttttgtgcaattctcactg--------tcggtactgaaaccaaacttttcagGAGCACCTATTTATCGTCTGTGAGCTACTACGAGCTAATCTGTACGAGTTTCACAAGTACAACCGAGATTCGGGAGGGGAGGTCTATTTCACGATGCCTA

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|162242877|gb|FC415307.1|FC415307
EST:     CTACTTTTACCACCGG                         GAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTT
genomic: CTACTTTTACCACCGGgtaattaggg ... gtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgcctttggtttatataggtaagcgctaaatattggtggtggtgattgtagGAGCACCTGTTCATCGTTTGTGAGTTACTTCGAGCTAACCTATACGAGTTTCATAAATACAACAGAGAATCAGGTGGCGAGGTGTACTTTACGATGCCCC
                           cgctaaa  putative branch site (score: 3)
             tttatata  TA-rich tract